0.1 Импорт

Импорт phyloseq объекта и библиотек
Датасет - хроносерия разложения соломы - от фактор Day 10ти уровней

library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(ANCOMBC)
library(heatmaply)
library(compositions)
library(igraph)
library(WGCNA)
require(DESeq2)
require(phyloseq)

ps.f <- readRDS("psf2")

0.2 functions

#phyloseq object to ampvis2 object
#https://gist.github.com/KasperSkytte/8d0ca4206a66be7ff6d76fc4ab8e66c6

phyloseq_to_ampvis2 <- function(physeq) {
  #check object for class
  if(!any(class(physeq) %in% "phyloseq"))
    stop("physeq object must be of class \"phyloseq\"", call. = FALSE)
  
  #ampvis2 requires taxonomy and abundance table, phyloseq checks for the latter
  if(is.null(physeq@tax_table))
    stop("No taxonomy found in the phyloseq object and is required for ampvis2", call. = FALSE)
  
  #OTUs must be in rows, not columns
  if(phyloseq::taxa_are_rows(physeq))
    abund <- as.data.frame(phyloseq::otu_table(physeq)@.Data)
  else
    abund <- as.data.frame(t(phyloseq::otu_table(physeq)@.Data))
  
  #tax_table is assumed to have OTUs in rows too
  tax <- phyloseq::tax_table(physeq)@.Data
  
  #merge by rownames (OTUs)
  otutable <- merge(
    abund,
    tax,
    by = 0,
    all.x = TRUE,
    all.y = FALSE,
    sort = FALSE
  )
  colnames(otutable)[1] <- "OTU"
  
  #extract sample_data (metadata)
  if(!is.null(physeq@sam_data)) {
    metadata <- data.frame(
      phyloseq::sample_data(physeq),
      row.names = phyloseq::sample_names(physeq), 
      stringsAsFactors = FALSE, 
      check.names = FALSE
    )
    
    #check if any columns match exactly with rownames
    #if none matched assume row names are sample identifiers
    samplesCol <- unlist(lapply(metadata, function(x) {
      identical(x, rownames(metadata))}))
    
    if(any(samplesCol)) {
      #error if a column matched and it's not the first
      if(!samplesCol[[1]])
        stop("Sample ID's must be in the first column in the sample metadata, please reorder", call. = FALSE)
    } else {
      #assume rownames are sample identifiers, merge at the end with name "SampleID"
      if(any(colnames(metadata) %in% "SampleID"))
        stop("A column in the sample metadata is already named \"SampleID\" but does not seem to contain sample ID's", call. = FALSE)
      metadata$SampleID <- rownames(metadata)
      
      #reorder columns so SampleID is the first
      metadata <- metadata[, c(which(colnames(metadata) %in% "SampleID"), 1:(ncol(metadata)-1L)), drop = FALSE]
    }
  } else
    metadata <- NULL
  
  #extract phylogenetic tree, assumed to be of class "phylo"
  if(!is.null(physeq@phy_tree)) {
    tree <- phyloseq::phy_tree(physeq)
  } else
    tree <- NULL
  
  #extract OTU DNA sequences, assumed to be of class "XStringSet"
  if(!is.null(physeq@refseq)) {
    #convert XStringSet to DNAbin using a temporary file (easiest)
    fastaTempFile <- tempfile(pattern = "ampvis2_", fileext = ".fa")
    Biostrings::writeXStringSet(physeq@refseq, filepath = fastaTempFile)
  } else
    fastaTempFile <- NULL
  
  #load as normally with amp_load
  ampvis2::amp_load(
    otutable = otutable,
    metadata = metadata,
    tree = tree,
    fasta = fastaTempFile
  )
}

#variance stabilisation from DESeq2

ps_vst <- function(ps, factor){
  

  
  diagdds = phyloseq_to_deseq2(ps, as.formula(paste( "~", factor)))              
  diagdds = estimateSizeFactors(diagdds, type="poscounts")
  diagdds = estimateDispersions(diagdds, fitType = "local") 
  pst <- varianceStabilizingTransformation(diagdds)
  pst.dimmed <- t(as.matrix(assay(pst))) 
  # pst.dimmed[pst.dimmed < 0.0] <- 0.0
  ps.varstab <- ps
  otu_table(ps.varstab) <- otu_table(pst.dimmed, taxa_are_rows = FALSE) 
  return(ps.varstab)
}

#WGCNA visualisation
#result - list class object with attributes:
# ps - phyloseq object
# amp - ampwis2 object
# heat - heatmap with absalute read numbers
# heat_rel - hetmap with relative abundances
# tree - phylogenetic tree with taxonomy

color_filt <- function(ps, df){
  
      library(tidyverse)
      library(reshape2)
      library(gridExtra)

  
  l = list()
  for (i in levels(df$module)){
    message(i)
    color_name <-  df %>% 
      filter(module == i) %>% 
      pull(asv) %>% 
      unique()
    ps.col <- prune_taxa(color_name, ps)
    amp.col <- phyloseq_to_ampvis2(ps.col)
    heat <- amp_heatmap(amp.col, tax_show = 60, 
              group_by = "Day", 
              tax_aggregate = "OTU",
              tax_add = "Genus", 
              normalise=FALSE, 
              showRemainingTaxa = TRUE)
    
    ps.rel  <-  phyloseq::transform_sample_counts(ps.col, function(x) x / sum(x) * 100)
    amp.r <- phyloseq_to_ampvis2(ps.rel)
    heat.rel <- amp_heatmap(amp.r, tax_show = 60, 
          group_by = "Day", 
          tax_aggregate = "OTU",
          tax_add = "Genus", 
          normalise=FALSE, 
          showRemainingTaxa = TRUE)
    
    tree <- ps.col@phy_tree
    taxa <- as.data.frame(ps.col@tax_table@.Data)
    p1 <- ggtree(tree) + 
              geom_tiplab(size=2, align=TRUE, linesize=.5) +
              theme_tree2()
    
    taxa[taxa == "Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium"] <- "Allorhizobium"
    taxa[taxa == "Burkholderia-Caballeronia-Paraburkholderia"] <- "Burkholderia"
  
    tx <- taxa %>% 
      rownames_to_column("id") %>% 
      mutate(id = factor(id, levels = rev(get_taxa_name(p1)))) %>% 
      dplyr::select(-c(Kingdom, Species, Order)) %>% 
      melt(id.var = 'id')

    p2 <- ggplot(tx, aes(variable, id)) + 
      geom_tile(aes(fill = value), alpha = 0.4) +
      geom_text(aes(label = value), size = 3) +
      theme_bw() + 
      theme(legend.position = "none",
             axis.ticks.x=element_blank(),
             axis.text.y=element_blank(),
             axis.ticks.y=element_blank(),
             axis.title.x = element_blank(),
            axis.title.y = element_blank()) 

    p <- ggpubr::ggarrange(p1, p2, widths = c(0.9, 1))
    l[[i]] <- list("ps" = ps.col, 
                   "amp" = amp.col,
                   "heat" = heat,
                   "heat_rel" = heat.rel,
                   "tree" = p,
                   "taxa" = knitr::kable(taxa))
                    
  }
  return(l)
}

detachAllPackages <- function() {

  basic.packages <- c("package:stats","package:graphics","package:grDevices","package:utils","package:datasets","package:methods","package:base")

  package.list <- search()[ifelse(unlist(gregexpr("package:",search()))==1,TRUE,FALSE)]

  package.list <- setdiff(package.list,basic.packages)

  if (length(package.list)>0)  for (package in package.list) detach(package, character.only=TRUE, force = TRUE)

}

plot_alpha_w_toc <- function(ps, group, metric) {
  
  require(phyloseq)
  require(ggplot2)
  
  ps_a <- prune_taxa(taxa_sums(ps) > 0, ps)
  
  er <- estimate_richness(ps_a)
  df_er <- cbind(ps_a@sam_data, er)
  df_er <- df_er %>% select(c(group, metric))
  stat.test <- aov(as.formula(paste0(metric, "~", group)), data = df_er) %>%
    rstatix::tukey_hsd()
  y <-  seq(max(er[[metric]]), length=length(stat.test$p.adj), by=max(er[[metric]]/20))

  plot_richness(ps_a, x=group, measures=metric) + 
    geom_boxplot() +
    geom_point(size=1.2, alpha=0.3) +
    ggpubr::stat_pvalue_manual(
      stat.test, 
      label = "p.adj.signif", 
      y.position = y) +
    theme_light() + 
    scale_color_brewer(palette="Dark2") +
    theme(axis.text.x = element_text(angle = 90),
          axis.title.x=element_blank()) +
    labs(y=paste(metric, "index")) 
}


# standart NMDS plot tool frop phyloseq with some additional aestatics 
# have stress value on plot - may work as fuck
beta_custom_norm_NMDS_elli_w <- function(ps, seed = 7888, normtype="vst", Color="What", Group="Repeat"){
  require(phyloseq)
  require(ggplot2)
  require(ggpubr)
  library(ggforce)
  
  
  ordination.b <- ordinate(ps, "NMDS", "bray")
  mds <- as.data.frame(ordination.b$points)
  p  <-  plot_ordination(ps,
                         ordination.b,
                         type="sample",
                         color = Color,
                         title="NMDS - Bray-Curtis",
                         # title=NULL,
                         axes = c(2,3) ) + 
    theme_bw() + 
    theme(text = element_text(size = 10)) + 
    geom_point(size = 3) +
    annotate("text",
    x=min(mds$MDS1) + abs(min(mds$MDS1))/7,
    y=max(mds$MDS2),
    label=paste0("Stress -- ", round(ordination.b$stress, 3))) +
    geom_mark_ellipse(aes_string(group = Group, label = Group),
                      label.fontsize = 10,
                      label.buffer = unit(2, "mm"),
                      label.minwidth = unit(5, "mm"),
                      con.cap = unit(0.1, "mm"),
                      con.colour='gray') +
    theme(legend.position = "none") +
    ggplot2::scale_fill_viridis_c(option = "H")
  
  return(p)
}


# alpha with aov + tukie post-hock - useless, but it looks pretty good
plot_alpha_w_toc <- function(ps, group, metric) {
  
  require(phyloseq)
  require(ggplot2)
  
  ps_a <- prune_taxa(taxa_sums(ps) > 0, ps)
  
  er <- estimate_richness(ps_a)
  df_er <- cbind(ps_a@sam_data, er)
  df_er <- df_er %>% select(c(group, metric))
  stat.test <- aov(as.formula(paste0(metric, "~", group)), data = df_er) %>%
    rstatix::tukey_hsd()
  y <- seq(max(er[[metric]]), length=length(stat.test$p.adj.signif[stat.test$p.adj.signif != "ns"]), by=max(er[[metric]]/20))
  
  plot_richness(ps_a, x=group, measures=metric) + 
    geom_boxplot() +
    geom_point(size=1.2, alpha=0.3) +
    stat_pvalue_manual(
      stat.test, 
      label = "p.adj.signif", 
      y.position = y,
      hide.ns=TRUE) +
    theme_light() + 
    scale_color_brewer(palette="Dark2") +
    theme(axis.text.x = element_text(angle = 90),
          axis.title.x=element_blank()) +
    labs(y=paste(metric, "index")) 
}

0.3 Alpha

p1 <- plot_alpha_w_toc(ps = ps.f, group = "Day", metric = "Observed")
## Note: Using an external vector in selections is ambiguous.
## ℹ Use `all_of(group)` instead of `group` to silence this message.
## ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.
## Note: Using an external vector in selections is ambiguous.
## ℹ Use `all_of(metric)` instead of `metric` to silence this message.
## ℹ See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.
p2 <- plot_alpha_w_toc(ps = ps.f, group = "Day", metric = "Shannon")
p3 <- plot_alpha_w_toc(ps = ps.f, group = "Day", metric = "InvSimpson")
ggarrange(p1, p2, p3, nrow = 1)

Add Group parameter to metadata -
- early - D01, D03, D05
- middle - D07, D08, D10
- late - D13, D14, D15

sample.data <- ps.f@sam_data %>% 
  data.frame() %>% 
  mutate(Group = if_else(Day %in% c("D01", "D03", "D05"), "early", 
                         if_else(Day %in% c("D07", "D08","D10"), "middle", "late"))) %>% 
  mutate(Group = factor(Group, levels=c("early", "middle","late"))) %>% 
  phyloseq::sample_data()

sample_data(ps.f) <- sample.data

p.observed <- plot_alpha_w_toc(ps = ps.f, group = "Group", metric = c("Observed")) + 
  theme(axis.title.y = element_blank())

p.shannon <- plot_alpha_w_toc(ps = ps.f, group = "Group", metric = c("Shannon")) + 
  theme(axis.title.y = element_blank())

p.simpson <- plot_alpha_w_toc(ps = ps.f, group = "Group", metric = c("InvSimpson")) + 
  theme(axis.title.y = element_blank())

ggpubr::ggarrange(p.observed, p.shannon, p.simpson, ncol = 3)

0.4 beta statistic

0.4.1 permanova

permanova - group significantlly different - dispersion between is more, than inside groups

dist <- phyloseq::distance(ps.f, "bray")
metadata <- as(sample_data(ps.f@sam_data), "data.frame")
vegan::adonis2(dist ~ Group, data = metadata)
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
## 
## vegan::adonis2(formula = dist ~ Group, data = metadata)
##          Df SumOfSqs      R2      F Pr(>F)    
## Group     2   3.2742 0.33893 8.2033  0.001 ***
## Residual 32   6.3861 0.66107                  
## Total    34   9.6604 1.00000                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

0.4.2 dynamic of beta diversity

Дистанция брей кертиса по шагам между каждыми днями.   (Например - все D15 против D14)   Может на эту картинку подвесить еще почвенное дыхание?

ps.f.r <- rarefy_even_depth(ps.f, rngseed = 777)

avg.r <- ps.f.r@otu_table %>% 
  as.data.frame() %>%
  vegan::avgdist(10)

avg <- ps.f@otu_table %>% 
  as.data.frame() %>%
  vegan::avgdist(10)

# avg %>%
#   as.matrix() %>%
#   as_tibble(rownames= "sample") %>%
#   pivot_longer(-sample) %>%
#   filter(sample < name) %>%
#   mutate(repeat_a = str_replace(sample, ".*-", ""),
#          repeat_b = str_replace(name, ".*-", ""), 
#          day_a = as.numeric(str_replace(sapply(strsplit(sample, "-"), `[`, 3), "D", "")),
#           day_b = as.numeric(str_replace(sapply(strsplit(name, "-"), `[`, 3), "D", "")),
#          diff = abs(day_a - day_b),
#          early = day_a < 10) %>% 
#   filter(repeat_a == repeat_b & diff < 10) %>%
#   group_by(diff, repeat_a, early) %>%
#   summarize(median = median(value)) %>%
#   ungroup() %>%
#   ggplot(aes(x=diff, y=median, color=early, group=paste0(repeat_a, early))) +
#   geom_line(size=0.25) +
#   geom_smooth(aes(group=early), se=FALSE, size=4) +
#   labs(x="Distance between time points",
#        y="Median Bray-Curtis distance") +
#   scale_x_continuous(breaks=1:9) +
#   scale_color_manual(name=NULL,
#                      breaks=c(TRUE, FALSE),
#                      values=c("blue", "red"),
#                      labels=c("Early", "Late")) +
#   guides(color = guide_legend(override.aes = list(size=1))) +
#   theme_classic()

avg.r %>%
  as.matrix() %>%
  as_tibble(rownames= "sample") %>%
  pivot_longer(-sample) %>%
  filter(sample < name) %>%
  mutate(repeat_a = str_replace(sample, ".*-", ""),
         repeat_b = str_replace(name, ".*-", ""), 
         day_a = as.numeric(str_replace(sapply(strsplit(sample, "-"), `[`, 3), "D", "")),
          day_b = as.numeric(str_replace(sapply(strsplit(name, "-"), `[`, 3), "D", ""))) %>% 
  mutate(day_a = as.numeric(as.factor(day_a) %>% forcats::fct_recode("2" = "3", "3" = "5", "4" = "7", "5" = "8", "6" = "10", "7" = "13", "8" = "14", "9" = "14", "10" = "15")),
         day_b = as.numeric(as.factor(day_b) %>% forcats::fct_recode("2" = "3", "3" = "5", "4" = "7", "5" = "8", "6" = "10", "7" = "12", "8" = "13", "9" = "14", "10" = "15")),
         diff = abs(day_a - day_b)) %>% 
  filter(diff == 1) %>% 
  mutate(day_b = as.factor(day_b) %>% forcats::fct_recode("D03" = "2", "D05" = "3","D07" = "4",  "D08" = "5", "D10" = "6", "D13" = "7", "D14" = "8", "D15" = "10", "D12" = "7")) %>% 
  ggplot(aes(x=day_b, y=value)) +
    geom_boxplot() +
  theme_bw() +
  labs(x="Time points",
       y="Bray-Curtis distance")

0.4.3 basic NMDS plot

IN WORK!!

beta_custom_norm_NMDS_elli_w(ps.f, C="Group", G="Day")
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.1048129 
## Run 1 stress 0.1372731 
## Run 2 stress 0.1318495 
## Run 3 stress 0.1048129 
## ... Procrustes: rmse 0.00004856956  max resid 0.0001949092 
## ... Similar to previous best
## Run 4 stress 0.1048129 
## ... New best solution
## ... Procrustes: rmse 0.00001842645  max resid 0.00006948497 
## ... Similar to previous best
## Run 5 stress 0.1426236 
## Run 6 stress 0.1048204 
## ... Procrustes: rmse 0.001770292  max resid 0.007527799 
## ... Similar to previous best
## Run 7 stress 0.1064532 
## Run 8 stress 0.1064733 
## Run 9 stress 0.1048204 
## ... Procrustes: rmse 0.001767644  max resid 0.007510715 
## ... Similar to previous best
## Run 10 stress 0.1064532 
## Run 11 stress 0.1318495 
## Run 12 stress 0.1064733 
## Run 13 stress 0.1064733 
## Run 14 stress 0.1460032 
## Run 15 stress 0.1048204 
## ... Procrustes: rmse 0.001769848  max resid 0.007525048 
## ... Similar to previous best
## Run 16 stress 0.1064532 
## Run 17 stress 0.1372728 
## Run 18 stress 0.1048129 
## ... Procrustes: rmse 0.000002711789  max resid 0.0000100797 
## ... Similar to previous best
## Run 19 stress 0.1460029 
## Run 20 stress 0.146003 
## *** Solution reached

0.5 Splitting the dataset

Разделим датасет на две группы

1-я - в более чем 10% образцов должно быть хотя бы 10 ридов - эта группа пойдет в анализ далее

ps.inall <- phyloseq::filter_taxa(ps.f, function(x) sum(x > 10) > (0.1*length(x)), TRUE)
amp.inall <- phyloseq_to_ampvis2(ps.inall)
amp_heatmap(amp.inall,
            tax_show = 40,
            group_by = "Day",
            tax_aggregate = "OTU",
            tax_add = "Genus",
            normalise=FALSE,
            showRemainingTaxa = TRUE)

Вторая - оставшиеся, но более 100 ридов по всем образцам(далее - вылетающие мажоры(ВМ))
Остальные филотипы выкидываем из анализа

ps.exl  <- phyloseq::filter_taxa(ps.f, function(x) sum(x > 10) < (0.1*length(x)), TRUE)
ps.exl  <- prune_taxa(taxa_sums(ps.exl) > 100, ps.exl)
amp.exl <- phyloseq_to_ampvis2(ps.exl)
amp_heatmap(amp.exl,
            tax_show = 40,
            group_by = "Day",
            tax_aggregate = "OTU",
            tax_add = "Genus",
            normalise=FALSE,
            showRemainingTaxa = TRUE)

То же, но c относительной представленностью.

ps.per  <-  phyloseq::transform_sample_counts(ps.f, function(x) x / sum(x) * 100) 
ps.exl.taxa <- taxa_names(ps.exl)
ps.per.exl <- prune_taxa(ps.exl.taxa, ps.per)
amp.exl.r <- phyloseq_to_ampvis2(ps.per.exl)

amp_heatmap(amp.exl.r, tax_show = 60, 
      group_by = "Day", 
      tax_aggregate = "OTU",
      tax_add = "Genus", 
      round =  2, 
      normalise=FALSE, 
      showRemainingTaxa = TRUE)

amp_heatmap(amp.exl.r, tax_show = 60, 
      group_by = "Day", 
      tax_aggregate = "OTU",
      tax_add = "Genus", 
      round =  2, 
      normalise=FALSE, )

ВМ объединенные по родам. Относительная представленность.

amp_heatmap(amp.exl.r,
            tax_show = 30, 
            group_by = "Day", 
            tax_aggregate = "Genus",
            tax_add = "Phylum",
            tax_class = "Proteobacteria",
            round =  2,
            normalise=FALSE, 
            showRemainingTaxa = TRUE)

Если посмотреть, если как распределяются ВМ по дням - похоже распределение ВМ связано не только с особенностью отдельных мешочков, но и с чисто техническими особенностями - вылетающие значения вылетают в основном не с биологическими повторностями, а с техническими(красная линия - выбрана визуально)

p_box <- phyloseq::sample_sums(ps.per.exl) %>% 
  as.data.frame(col.names = "values") %>% 
  setNames(., nm = "values") %>% 
  rownames_to_column("samples") %>% 
  mutate(Day = sapply(strsplit(samples, "-"), `[`, 3)) %>% 
  ggplot(aes(x=Day, y=values, color=Day, fill = Day)) +
  geom_boxplot(aes(color=Day, fill = Day)) +
  geom_point(color = "black", position = position_dodge(width=0.2)) +
  geom_hline(yintercept = 10, colour = "red") +
  theme_bw() +
  theme(legend.position = "none")
     
p_box <- p_box + viridis::scale_color_viridis(option = "H", discrete = TRUE, direction=1, begin=0.1, end = 0.9, alpha = 0.5)

p_box + viridis::scale_fill_viridis(option = "H", discrete = TRUE, direction=1, begin=0.1, end = 0.9, alpha = 0.3)

0.6 WGCNA

0.6.1 clr

после clr нормализации / выглядит отвратительно попробуем нормализацию vst из DESeq2

otu.inall <- as.data.frame(ps.inall@otu_table@.Data) 
ps.inall.clr <- ps.inall
otu_table(ps.inall.clr) <- phyloseq::otu_table(compositions::clr(otu.inall), taxa_are_rows = FALSE)
data <- ps.inall.clr@otu_table@.Data %>% 
  as.data.frame()
rownames(data) <- as.character(ps.inall.clr@sam_data$Description)
powers <-  c(c(1:10), seq(from = 12, to=30, by=1))
sft <-  pickSoftThreshold(data, powerVector = powers, verbose = 5, networkType = "signed")
## pickSoftThreshold: will use block size 338.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 338 of 338
## Warning: executing %dopar% sequentially: no parallel backend registered
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
## 1      1    0.185  23.60         0.8790 168.0000 168.00000 172.000
## 2      2    0.199 -15.50         0.8970  87.6000  87.20000  95.100
## 3      3    0.518 -13.10         0.8580  47.3000  46.80000  55.900
## 4      4    0.390  -6.46         0.8050  26.5000  26.00000  34.500
## 5      5    0.262  -3.46         0.7820  15.4000  14.90000  22.300
## 6      6    0.232  -2.30         0.7770   9.2300   8.78000  15.000
## 7      7    0.251  -1.87         0.6990   5.7300   5.36000  10.500
## 8      8    0.319  -1.75         0.7570   3.6800   3.41000   7.620
## 9      9    0.527  -2.07         0.7770   2.4400   2.20000   5.890
## 10    10    0.648  -2.28         0.8490   1.6600   1.47000   4.690
## 11    12    0.827  -2.41         0.8970   0.8420   0.69300   3.190
## 12    13    0.793  -2.38         0.7930   0.6220   0.49000   2.700
## 13    14    0.277  -3.97         0.0914   0.4690   0.35500   2.320
## 14    15    0.282  -3.83         0.1000   0.3610   0.26100   2.010
## 15    16    0.894  -2.17         0.9030   0.2820   0.19800   1.770
## 16    17    0.905  -2.10         0.9080   0.2240   0.15000   1.560
## 17    18    0.922  -2.04         0.9240   0.1810   0.11500   1.390
## 18    19    0.927  -2.01         0.9230   0.1480   0.08820   1.250
## 19    20    0.938  -1.93         0.9370   0.1220   0.06780   1.130
## 20    21    0.946  -1.86         0.9470   0.1020   0.05260   1.020
## 21    22    0.315  -3.12         0.2220   0.0856   0.04140   0.926
## 22    23    0.303  -3.96         0.1560   0.0728   0.03270   0.844
## 23    24    0.307  -2.92         0.1940   0.0623   0.02590   0.772
## 24    25    0.303  -2.84         0.1800   0.0538   0.02060   0.708
## 25    26    0.921  -1.63         0.8990   0.0467   0.01650   0.657
## 26    27    0.892  -1.61         0.8650   0.0408   0.01320   0.622
## 27    28    0.155  -1.93        -0.0202   0.0359   0.01040   0.591
## 28    29    0.199  -2.77        -0.0228   0.0317   0.00841   0.563
## 29    30    0.199  -2.69        -0.0203   0.0282   0.00684   0.537
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")

0.6.2 vst

после vst нормализации

ps.varstab <- ps_vst(ps.inall, "Day")

data2 <- ps.varstab@otu_table@.Data %>% 
  as.data.frame()

rownames(data2) <- as.character(ps.varstab@sam_data$Description)
powers <-  c(seq(from = 1, to=10, by=0.5), seq(from = 11, to=20, by=1))
sft2 <-  pickSoftThreshold(data2, powerVector = powers, verbose = 5, networkType = "signed hybrid")
## pickSoftThreshold: will use block size 338.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 338 of 338
##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1    1.0    0.409 -1.05          0.704  50.100  45.60000  97.80
## 2    1.5    0.578 -1.07          0.895  30.900  27.00000  71.20
## 3    2.0    0.723 -1.15          0.942  20.300  17.90000  53.60
## 4    2.5    0.767 -1.24          0.871  14.000  12.00000  41.70
## 5    3.0    0.809 -1.31          0.909  10.000   7.86000  33.40
## 6    3.5    0.872 -1.31          0.958   7.380   5.39000  27.30
## 7    4.0    0.888 -1.30          0.968   5.580   3.76000  22.60
## 8    4.5    0.858 -1.36          0.910   4.320   2.67000  19.00
## 9    5.0    0.892 -1.36          0.943   3.400   1.94000  16.20
## 10   5.5    0.899 -1.38          0.954   2.720   1.41000  13.90
## 11   6.0    0.896 -1.39          0.962   2.210   1.07000  12.10
## 12   6.5    0.897 -1.33          0.962   1.820   0.84700  10.60
## 13   7.0    0.910 -1.30          0.970   1.520   0.65400   9.30
## 14   7.5    0.914 -1.31          0.966   1.280   0.51500   8.25
## 15   8.0    0.913 -1.28          0.954   1.090   0.41500   7.36
## 16   8.5    0.905 -1.28          0.937   0.938   0.34000   6.59
## 17   9.0    0.895 -1.30          0.913   0.813   0.27800   5.99
## 18   9.5    0.878 -1.33          0.900   0.709   0.23200   5.49
## 19  10.0    0.886 -1.34          0.894   0.624   0.19100   5.07
## 20  11.0    0.911 -1.31          0.928   0.491   0.12500   4.35
## 21  12.0    0.890 -1.29          0.894   0.396   0.08590   3.79
## 22  13.0    0.910 -1.26          0.918   0.325   0.06120   3.33
## 23  14.0    0.882 -1.25          0.856   0.272   0.04420   2.95
## 24  15.0    0.889 -1.19          0.864   0.230   0.03230   2.63
## 25  16.0    0.913 -1.18          0.893   0.198   0.02240   2.35
## 26  17.0    0.930 -1.16          0.912   0.172   0.01620   2.20
## 27  18.0    0.955 -1.19          0.947   0.151   0.01190   2.09
## 28  19.0    0.908 -1.21          0.896   0.134   0.00896   1.99
## 29  20.0    0.916 -1.21          0.906   0.120   0.00649   1.91
plot(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n", main = paste("Scale independence"))
text(sft2$fitIndices[,1], -sign(sft2$fitIndices[,3])*sft2$fitIndices[,2], labels=powers,cex=0.9,col="red")
abline(h=0.9,col="salmon")

# WGCNA, as old and not supported
detachAllPackages()
library(WGCNA)


net3 <- WGCNA::blockwiseModules(data2,
                          power=5.5,
                          TOMType="signed",
                          networkType="signed hybrid",
                          nThreads=0)


mergedColors2 <-  WGCNA::labels2colors(net3$colors, colorSeq = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))

plotDendroAndColors(
  net3$dendrograms[[1]],
  mergedColors2[net3$blockGenes[[1]]],
  "Module colors",
  dendroLabels = FALSE,
  hang = 0.03,
  addGuide = TRUE,
  guideHang = 0.05)

0.6.2.1 Импорт 2

library(phyloseq)
library(tidyverse)
library(ggpubr)
library(ampvis2)
library(heatmaply)
library(WGCNA)
library(phyloseq)
library(ggtree)
library(tidyverse)
library(KneeArrower)
modules_of_interest = mergedColors2 %>% 
  unique()

module_df <- data.frame(
  asv = names(net3$colors),
  colors = mergedColors2
)

# module_df[module_df == "yellow"] <- "salmon"

submod <-  module_df %>%
  subset(colors %in% modules_of_interest)

row.names(module_df) = module_df$asv

subexpr = as.data.frame(t(data2))[submod$asv,]

submod_df <- data.frame(subexpr) %>%
  mutate(
    asv = row.names(.)
  ) %>%
  pivot_longer(-asv) %>%
  mutate(
    module = module_df[asv,]$colors
  )

submod_df <- submod_df %>% 
  mutate(name = gsub("\\_.*","",submod_df$name)) %>% 
  group_by(name, asv) %>% 
  summarise(value = mean(value), asv = asv, module = module) %>% 
  relocate(c(asv, name, value, module)) %>% 
  ungroup() %>% 
  mutate(module = as.factor(module))

p <- submod_df %>% 
  ggplot(., aes(x=name, y=value, group=asv)) +
  geom_line(aes(color = module),
            alpha = 0.2) +
  theme_bw() +
  theme(
    axis.text.x = element_text(angle = 90),
    legend.position = "none") +
  facet_grid(rows = vars(module)) +
  labs(x = "treatment",
       y = "normalized expression")

p + scale_color_manual(values = levels(submod_df$module))

0.6.2.2 ordination

UNIFRAC - колбаска сужается

ps.inall.col <- ps.inall
df <- module_df %>% 
  rename("id" = "asv")
df <- df %>% 
  dplyr::select(-"id") %>% 
  mutate(colors = as.factor(colors))
taxa <- as.data.frame(ps.inall@tax_table@.Data)
tx <- cbind(taxa, df)
tx$colors <- factor(tx$colors, levels = c("salmon", "darkgreen", "cyan", "red", "blue", "plum"))
tax_table(ps.inall.col) <- tax_table(as.matrix(tx))
ord <- ordinate(ps.inall.col, "NMDS", "unifrac")
## Run 0 stress 0.0685455 
## Run 1 stress 0.05568715 
## ... New best solution
## ... Procrustes: rmse 0.04076806  max resid 0.2160826 
## Run 2 stress 0.06784429 
## Run 3 stress 0.05628488 
## Run 4 stress 0.05568719 
## ... Procrustes: rmse 0.0001769095  max resid 0.0006062451 
## ... Similar to previous best
## Run 5 stress 0.07937976 
## Run 6 stress 0.07544596 
## Run 7 stress 0.05628489 
## Run 8 stress 0.05568719 
## ... Procrustes: rmse 0.00002559041  max resid 0.00008856774 
## ... Similar to previous best
## Run 9 stress 0.05568712 
## ... New best solution
## ... Procrustes: rmse 0.00002106782  max resid 0.00006934972 
## ... Similar to previous best
## Run 10 stress 0.06740137 
## Run 11 stress 0.06740136 
## Run 12 stress 0.06784421 
## Run 13 stress 0.06784436 
## Run 14 stress 0.06854546 
## Run 15 stress 0.07953205 
## Run 16 stress 0.05568719 
## ... Procrustes: rmse 0.00004255519  max resid 0.0001401031 
## ... Similar to previous best
## Run 17 stress 0.06740138 
## Run 18 stress 0.06728216 
## Run 19 stress 0.05568718 
## ... Procrustes: rmse 0.0000373923  max resid 0.0001312747 
## ... Similar to previous best
## Run 20 stress 0.07888487 
## *** Solution reached
plot_ordination(ps.inall.col, ord, type = "species", color = "colors") + 
  scale_color_manual(values =  c("salmon", "darkgreen", "cyan", "red", "blue", "plum")) +
  theme_bw() +
  theme(legend.position = "none")

Bray - колбаска равномерна
Поздние стадии слева - при этом ранние кластеры накладываются, поздние разделены Что влияет на ось2? Явно есть какой-то паттерн.

ord <- ordinate(ps.inall.col, "NMDS", "bray")
## Square root transformation
## Wisconsin double standardization
## Run 0 stress 0.09036937 
## Run 1 stress 0.0903694 
## ... Procrustes: rmse 0.00001927814  max resid 0.00007086537 
## ... Similar to previous best
## Run 2 stress 0.09024752 
## ... New best solution
## ... Procrustes: rmse 0.003386048  max resid 0.01505777 
## Run 3 stress 0.09036938 
## ... Procrustes: rmse 0.003390695  max resid 0.01505826 
## Run 4 stress 0.09036937 
## ... Procrustes: rmse 0.003386035  max resid 0.01507802 
## Run 5 stress 0.09036937 
## ... Procrustes: rmse 0.003386432  max resid 0.01505862 
## Run 6 stress 0.1257473 
## Run 7 stress 0.09036937 
## ... Procrustes: rmse 0.003385691  max resid 0.01507976 
## Run 8 stress 0.1268919 
## Run 9 stress 0.09036944 
## ... Procrustes: rmse 0.003410952  max resid 0.01523599 
## Run 10 stress 0.09024752 
## ... New best solution
## ... Procrustes: rmse 0.00003844186  max resid 0.0001638862 
## ... Similar to previous best
## Run 11 stress 0.09036937 
## ... Procrustes: rmse 0.003380784  max resid 0.0150593 
## Run 12 stress 0.09036938 
## ... Procrustes: rmse 0.003379871  max resid 0.01508219 
## Run 13 stress 0.09036939 
## ... Procrustes: rmse 0.003385498  max resid 0.01512324 
## Run 14 stress 0.1358024 
## Run 15 stress 0.09024754 
## ... Procrustes: rmse 0.00003794727  max resid 0.0001665169 
## ... Similar to previous best
## Run 16 stress 0.1258672 
## Run 17 stress 0.1358024 
## Run 18 stress 0.09036937 
## ... Procrustes: rmse 0.003376715  max resid 0.01503468 
## Run 19 stress 0.126985 
## Run 20 stress 0.1360016 
## *** Solution reached
plot_ordination(ps.inall.col, ord, type = "species", color = "colors") + 
  scale_color_manual(values =  c("salmon", "darkgreen", "cyan", "red", "blue", "plum")) +
  theme_bw() +
  theme(legend.position = "none")

0.6.2.3 visualisation

Далее идут одинаковые картинки по всем группам.

l_vst <- color_filt(ps.inall, submod_df)
l_vst

$blue \(blue\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 86 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 86 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 86 tips and 85 internal nodes ] refseq() DNAStringSet: [ 86 reference sequences ]

\(blue\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 86 89493 0 11387 1819 Avg#Reads 2556.94

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 86(100%) 86(100%) 86(100%) 85(98.84%) 79(91.86%) 50(58.14%) 7(8.14%)

Metadata variables: 4 SampleID, Day, Description, Group

\(blue\)heat \(blue\)heat_rel \(blue\)tree \(blue\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq314 Bacteria Cyanobacteria Vampirivibrionia Obscuribacterales Obscuribacteraceae NA NA
Seq23 Bacteria Cyanobacteria Vampirivibrionia Obscuribacterales Obscuribacteraceae NA NA
Seq65 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas NA
Seq188 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella soli
Seq334 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq75 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq167 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella massiliensis
Seq273 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Kaistiaceae Kaistia NA
Seq131 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudolabrys NA
Seq138 Bacteria Proteobacteria Alphaproteobacteria Micropepsales Micropepsaceae NA NA
Seq104 Bacteria Proteobacteria Alphaproteobacteria Micropepsales Micropepsaceae NA NA
Seq129 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Altererythrobacter NA
Seq28 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Devosiaceae Devosia NA
Seq360 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Mesorhizobium NA
Seq292 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae NA NA
Seq166 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Hyphomonadaceae Hirschia NA
Seq39 Bacteria Gemmatimonadota Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae NA NA
Seq30 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Conexibacter NA
Seq151 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales 67-14 NA NA
Seq250 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales 67-14 NA NA
Seq135 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq46 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq35 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq106 Bacteria Myxococcota Polyangia Polyangiales Sandaracinaceae NA NA
Seq345 Bacteria Bdellovibrionota Oligoflexia 0319-6G20 NA NA NA
Seq198 Bacteria Bdellovibrionota Bdellovibrionia Bdellovibrionales Bdellovibrionaceae Bdellovibrio NA
Seq97 Bacteria Bdellovibrionota Bdellovibrionia Bdellovibrionales Bdellovibrionaceae Bdellovibrio NA
Seq183 Bacteria Dependentiae Babeliae Babeliales UBA12409 NA NA
Seq424 Bacteria Actinobacteriota Actinobacteria Propionibacteriales Nocardioidaceae Kribbella NA
Seq136 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Iamiaceae Iamia NA
Seq174 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Iamiaceae Iamia NA
Seq43 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Galbitalea NA
Seq420 Bacteria Actinobacteriota Actinobacteria Micromonosporales Micromonosporaceae Luedemannella NA
Seq127 Bacteria Actinobacteriota Actinobacteria Micromonosporales Micromonosporaceae Dactylosporangium NA
Seq288 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae NA NA
Seq449 Bacteria Actinobacteriota Actinobacteria Propionibacteriales Propionibacteriaceae Jiangella NA
Seq91 Bacteria Bacteroidota Bacteroidia Bacteroidales NA NA NA
Seq149 Bacteria Bacteroidota Bacteroidia Bacteroidetes VC2.1 Bac22 NA NA NA
Seq169 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter calamicampi
Seq81 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq211 Bacteria Bacteroidota Bacteroidia NA NA NA NA
Seq119 Bacteria Bacteroidota Bacteroidia Sphingobacteriales env.OPS 17 NA NA
Seq77 Bacteria Spirochaetota Spirochaetia Spirochaetales Spirochaetaceae Salinispira NA
Seq175 Bacteria Spirochaetota Spirochaetia Spirochaetales Spirochaetaceae Spirochaeta 2 NA
Seq305 Bacteria Chloroflexi Anaerolineae Anaerolineales Anaerolineaceae NA NA
Seq379 Bacteria Chloroflexi Chloroflexia Chloroflexales Roseiflexaceae NA NA
Seq165 Bacteria Chloroflexi Chloroflexia Chloroflexales Roseiflexaceae NA NA
Seq327 Bacteria Chloroflexi Chloroflexia Thermomicrobiales JG30-KF-CM45 NA NA
Seq252 Bacteria Armatimonadota Fimbriimonadia Fimbriimonadales Fimbriimonadaceae NA NA
Seq382 Bacteria Verrucomicrobiota Verrucomicrobiae Pedosphaerales Pedosphaeraceae NA NA
Seq123 Bacteria Verrucomicrobiota Verrucomicrobiae Opitutales Opitutaceae Lacunisphaera limnophila
Seq124 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq325 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Chthoniobacteraceae LD29 NA
Seq272 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Roseimicrobium gellanilyticum
Seq402 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Rubritaleaceae Luteolibacter NA
Seq322 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq356 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq259 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae Pir4 lineage NA
Seq279 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae Pir4 lineage NA
Seq214 Bacteria Planctomycetota Planctomycetes Planctomycetales Rubinisphaeraceae SH-PL14 NA
Seq209 Bacteria Planctomycetota Planctomycetes Planctomycetales Schlesneriaceae Schlesneria NA
Seq229 Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales Vicinamibacteraceae NA NA
Seq275 Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales Vicinamibacteraceae NA NA
Seq247 Bacteria Acidobacteriota Vicinamibacteria Vicinamibacterales NA NA NA
Seq316 Bacteria Bacteroidota Kapabacteria Kapabacteriales NA NA NA
Seq371 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq12 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq153 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq326 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq10 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae NA NA
Seq82 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Terrimonas NA
Seq462 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq150 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Flavitalea NA
Seq290 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq339 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq120 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq233 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales 211ds20 NA NA
Seq133 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter flavus
Seq349 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter NA
Seq315 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq57 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq96 Bacteria Proteobacteria Gammaproteobacteria R7C24 NA NA NA
Seq170 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq94 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Dokdonella ginsengisoli
Seq114 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq235 Bacteria Proteobacteria Gammaproteobacteria Legionellales Legionellaceae Legionella NA

$cyan \(cyan\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 30 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 30 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 30 tips and 29 internal nodes ] refseq() DNAStringSet: [ 30 reference sequences ]

\(cyan\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 30 176073 336 15108 4911 Avg#Reads 5030.66

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 30(100%) 30(100%) 30(100%) 30(100%) 30(100%) 29(96.67%) 2(6.67%)

Metadata variables: 4 SampleID, Day, Description, Group

\(cyan\)heat \(cyan\)heat_rel \(cyan\)tree \(cyan\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq98 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Burkholderia telluris
Seq64 Bacteria Proteobacteria Alphaproteobacteria Azospirillales Inquilinaceae Inquilinus ginsengisoli
Seq4 Bacteria Proteobacteria Alphaproteobacteria Azospirillales Inquilinaceae Inquilinus NA
Seq244 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudorhodoplanes NA
Seq11 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium NA
Seq74 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium NA
Seq22 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Starkeya NA
Seq45 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq9 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq29 Bacteria Myxococcota Polyangia Nannocystales Nannocystaceae Nannocystis NA
Seq239 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Labilithrix NA
Seq50 Bacteria Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium NA
Seq34 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Streptosporangiaceae Herbidospora NA
Seq56 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq25 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Terribacillus NA
Seq3 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq5 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq13 Bacteria Firmicutes Bacilli Bacillales Planococcaceae NA NA
Seq7 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Solibacillus NA
Seq19 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Solibacillus NA
Seq17 Bacteria Planctomycetota Planctomycetes Isosphaerales Isosphaeraceae Singulisphaera NA
Seq324 Bacteria Acidobacteriota Acidobacteriae Acidobacteriales Acidobacteriaceae (Subgroup 1) Edaphobacter NA
Seq16 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq6 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq1 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq109 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq49 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq73 Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomaceae Dyadobacter NA
Seq15 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Luteibacter NA
Seq26 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas NA

$darkgreen \(darkgreen\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 44 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 44 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 44 tips and 43 internal nodes ] refseq() DNAStringSet: [ 44 reference sequences ]

\(darkgreen\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 44 12360 0 2468 65 Avg#Reads 353.14

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 44(100%) 44(100%) 44(100%) 43(97.73%) 40(90.91%) 24(54.55%) 3(6.82%)

Metadata variables: 4 SampleID, Day, Description, Group

\(darkgreen\)heat \(darkgreen\)heat_rel \(darkgreen\)tree \(darkgreen\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq342 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae NA NA
Seq196 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae Candidatus Nitrocosmicus NA
Seq276 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae NA NA
Seq419 Archaea Crenarchaeota Nitrososphaeria Nitrososphaerales Nitrososphaeraceae NA NA
Seq454 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae Aquicella NA
Seq329 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas jaspsi
Seq332 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Magnetospiraceae NA NA
Seq429 Bacteria Proteobacteria Alphaproteobacteria Acetobacterales Acetobacteraceae NA NA
Seq195 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudorhodoplanes NA
Seq144 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudolabrys NA
Seq369 Bacteria Proteobacteria Alphaproteobacteria Micropepsales Micropepsaceae NA NA
Seq362 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Altererythrobacter NA
Seq428 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Phenylobacterium NA
Seq347 Bacteria Nitrospirota Nitrospiria Nitrospirales Nitrospiraceae Nitrospira japonica
Seq328 Bacteria Myxococcota Polyangia Haliangiales Haliangiaceae Haliangium NA
Seq348 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq308 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq256 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Minicystis NA
Seq302 Bacteria Bdellovibrionota Oligoflexia 0319-6G20 NA NA NA
Seq435 Bacteria Actinobacteriota Actinobacteria Propionibacteriales Propionibacteriaceae Microlunatus NA
Seq291 Bacteria Actinobacteriota Acidimicrobiia IMCC26256 NA NA NA
Seq392 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Ilumatobacteraceae NA NA
Seq321 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq186 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq204 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Paenisporosarcina NA
Seq146 Bacteria Spirochaetota Spirochaetia Spirochaetales Spirochaetaceae Spirochaeta 2 NA
Seq359 Bacteria Patescibacteria Saccharimonadia Saccharimonadales LWQ8 NA NA
Seq269 Bacteria Chloroflexi Chloroflexia Chloroflexales Roseiflexaceae NA NA
Seq267 Bacteria Verrucomicrobiota Verrucomicrobiae Opitutales Opitutaceae Lacunisphaera NA
Seq320 Bacteria Verrucomicrobiota Verrucomicrobiae Opitutales Opitutaceae Opitutus NA
Seq203 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq497 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq384 Bacteria Planctomycetota Planctomycetes Planctomycetales NA NA NA
Seq155 Bacteria Acidobacteriota Blastocatellia Blastocatellales Blastocatellaceae NA NA
Seq350 Bacteria Bacteroidota Bacteroidia Sphingobacteriales env.OPS 17 NA NA
Seq224 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Terrimonas NA
Seq409 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq337 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq494 Bacteria Bacteroidota Bacteroidia Cytophagales Amoebophilaceae Candidatus Amoebophilus NA
Seq277 Bacteria Proteobacteria Gammaproteobacteria NA NA NA NA
Seq191 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq335 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Luteimonas vadosa
Seq157 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Dokdonella NA
Seq385 Bacteria Proteobacteria Gammaproteobacteria Salinisphaerales Solimonadaceae NA NA

$plum \(plum\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 30 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 30 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 30 tips and 29 internal nodes ] refseq() DNAStringSet: [ 30 reference sequences ]

\(plum\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 30 17172 0 3034 103 Avg#Reads 490.63

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 30(100%) 30(100%) 30(100%) 30(100%) 27(90%) 16(53.33%) 1(3.33%)

Metadata variables: 4 SampleID, Day, Description, Group

\(plum\)heat \(plum\)heat_rel \(plum\)tree \(plum\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq161 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae Aquicella NA
Seq181 Bacteria Proteobacteria Gammaproteobacteria CCD24 NA NA NA
Seq207 Bacteria Cyanobacteria Vampirivibrionia Obscuribacterales Obscuribacteraceae NA NA
Seq219 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas naasensis
Seq216 Bacteria Proteobacteria Alphaproteobacteria Dongiales Dongiaceae Dongia NA
Seq220 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq90 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Pseudolabrys NA
Seq271 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae NA NA
Seq111 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingobium NA
Seq33 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Caulobacter NA
Seq189 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter NA
Seq85 Bacteria Myxococcota Polyangia Polyangiales BIrii41 NA NA
Seq208 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Galbitalea NA
Seq218 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter NA
Seq215 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq177 Bacteria Fibrobacterota Fibrobacteria Fibrobacterales Fibrobacteraceae NA NA
Seq375 Bacteria Chloroflexi Chloroflexia Thermomicrobiales JG30-KF-CM45 NA NA
Seq430 Bacteria Planctomycetota Phycisphaerae Phycisphaerales Phycisphaeraceae NA NA
Seq368 Bacteria Planctomycetota Planctomycetes Pirellulales Pirellulaceae NA NA
Seq152 Bacteria Planctomycetota Planctomycetes Gemmatales Gemmataceae Gemmata NA
Seq304 Bacteria Planctomycetota Planctomycetes Planctomycetales NA NA NA
Seq141 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Terrimonas NA
Seq343 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae NA NA
Seq412 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Edaphobaculum NA
Seq457 Bacteria Proteobacteria Gammaproteobacteria Coxiellales Coxiellaceae Coxiella NA
Seq130 Bacteria Proteobacteria Gammaproteobacteria R7C24 NA NA NA
Seq346 Bacteria Proteobacteria Gammaproteobacteria Salinisphaerales Solimonadaceae Alkanibacter NA
Seq474 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq472 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq227 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA

$red \(red\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 75 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 75 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 75 tips and 74 internal nodes ] refseq() DNAStringSet: [ 75 reference sequences ]

\(red\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 75 66650 241 5339 1528 Avg#Reads 1904.29

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 75(100%) 75(100%) 75(100%) 74(98.67%) 74(98.67%) 66(88%) 11(14.67%)

Metadata variables: 4 SampleID, Day, Description, Group

\(red\)heat \(red\)heat_rel \(red\)tree \(red\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq117 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Burkholderia NA
Seq60 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Alcaligenaceae NA NA
Seq121 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Variovorax NA
Seq383 Bacteria Proteobacteria Alphaproteobacteria Ferrovibrionales Ferrovibrionaceae Ferrovibrio soli
Seq228 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae NA NA
Seq178 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Methylobacterium-Methylorubrum NA
Seq171 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Bosea thiooxidans
Seq341 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Bosea NA
Seq89 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Tardiphaga robiniae
Seq31 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Starkeya NA
Seq160 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Hyphomicrobiaceae Hyphomicrobium NA
Seq251 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingopyxis NA
Seq373 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Altererythrobacter NA
Seq108 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Mesorhizobium NA
Seq71 Bacteria Actinobacteriota Thermoleophilia Solirubrobacterales Solirubrobacteraceae Conexibacter NA
Seq338 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Pajaroellobacter NA
Seq230 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Pajaroellobacter NA
Seq88 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Sorangium NA
Seq303 Bacteria Actinobacteriota Acidimicrobiia Microtrichales Ilumatobacteraceae NA NA
Seq93 Bacteria Actinobacteriota Actinobacteria Micrococcales Promicromonosporaceae Promicromonospora NA
Seq366 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Leifsonia NA
Seq134 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae NA aoyamense
Seq411 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Agromyces NA
Seq115 Bacteria Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium NA
Seq128 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Streptosporangiaceae Herbidospora mongoliensis
Seq398 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Streptosporangiaceae Nonomuraea NA
Seq78 Bacteria Actinobacteriota Actinobacteria Streptosporangiales Thermomonosporaceae Actinocorallia NA
Seq193 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq148 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Pedobacter NA
Seq307 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq431 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NS11-12 marine group NA NA
Seq205 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus lautus
Seq86 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq51 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq18 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq192 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq266 Bacteria Firmicutes Bacilli Paenibacillales Paenibacillaceae Paenibacillus NA
Seq278 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Domibacillus NA
Seq99 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Bacillus NA
Seq53 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Lysinibacillus NA
Seq118 Bacteria Firmicutes Bacilli Bacillales Planococcaceae Lysinibacillus NA
Seq76 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq232 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq168 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Terrimicrobiaceae Terrimicrobium NA
Seq387 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Chthoniobacteraceae Chthoniobacter NA
Seq285 Bacteria Verrucomicrobiota Verrucomicrobiae Chthoniobacterales Chthoniobacteraceae Chthoniobacter NA
Seq217 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Verrucomicrobium spinosum
Seq190 Bacteria Planctomycetota Planctomycetes Gemmatales Gemmataceae Gemmata NA
Seq249 Bacteria Planctomycetota Planctomycetes Isosphaerales Isosphaeraceae Singulisphaera NA
Seq254 Bacteria Acidobacteriota Acidobacteriae Acidobacteriales Acidobacteriaceae (Subgroup 1) Edaphobacter NA
Seq67 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq176 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq268 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq32 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq84 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq459 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq40 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella hibisci
Seq173 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq246 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq112 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Flavitalea NA
Seq126 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga ginsengihumi
Seq102 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga arvensicola
Seq309 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga soli
Seq70 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq262 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq301 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Taibaiella NA
Seq572 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae NA NA
Seq436 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter NA
Seq261 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq298 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq354 Bacteria Proteobacteria Gammaproteobacteria Gammaproteobacteria Incertae Sedis Unknown Family Acidibacter NA
Seq226 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Rhodanobacteraceae Tahibacter NA
Seq147 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Xanthomonas NA
Seq370 Bacteria Proteobacteria Gammaproteobacteria Diplorickettsiales Diplorickettsiaceae NA NA
Seq486 Bacteria Proteobacteria Gammaproteobacteria NA NA NA NA

$salmon \(salmon\)ps phyloseq-class experiment-level object otu_table() OTU Table: [ 73 taxa and 35 samples ] sample_data() Sample Data: [ 35 samples by 3 sample variables ] tax_table() Taxonomy Table: [ 73 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 73 tips and 72 internal nodes ] refseq() DNAStringSet: [ 73 reference sequences ]

\(salmon\)amp ampvis2 object with 5 elements. Summary of OTU table: Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads 35 73 115332 0 20534 779 Avg#Reads 3295.2

Assigned taxonomy: Kingdom Phylum Class Order Family Genus Species 73(100%) 73(100%) 73(100%) 72(98.63%) 71(97.26%) 66(90.41%) 12(16.44%)

Metadata variables: 4 SampleID, Day, Description, Group

\(salmon\)heat \(salmon\)heat_rel \(salmon\)tree \(salmon\)taxa

Kingdom Phylum Class Order Family Genus Species
Seq79 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Massilia armeniaca
Seq122 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae NA NA
Seq179 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Pseudoduganella NA
Seq145 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Pseudoduganella eburnea
Seq154 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Massilia NA
Seq222 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Oxalobacteraceae Massilia NA
Seq159 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Cupriavidus NA
Seq8 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Burkholderiaceae Cupriavidus NA
Seq14 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Alcaligenaceae Achromobacter NA
Seq54 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae NA paradoxus
Seq95 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Xylophilus NA
Seq340 Bacteria Proteobacteria Gammaproteobacteria Burkholderiales Comamonadaceae Rhizobacter NA
Seq264 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas mucosissima
Seq333 Bacteria Proteobacteria Alphaproteobacteria Reyranellales Reyranellaceae Reyranella NA
Seq158 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga NA
Seq248 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq245 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Devosiaceae Devosia neptuniae
Seq185 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Shinella NA
Seq156 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae NA NA
Seq42 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae NA NA
Seq286 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Ensifer NA
Seq21 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium NA
Seq107 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Neorhizobium NA
Seq231 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae Allorhizobium azooxidifex
Seq140 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae NA NA
Seq378 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Phenylobacterium mobile
Seq374 Bacteria Myxococcota Polyangia Haliangiales Haliangiaceae Haliangium NA
Seq257 Bacteria Myxococcota Polyangia Polyangiales Polyangiaceae Pajaroellobacter NA
Seq223 Bacteria Actinobacteriota Actinobacteria Micrococcales Promicromonosporaceae Cellulosimicrobium NA
Seq83 Bacteria Actinobacteriota Actinobacteria Micrococcales Microbacteriaceae Microbacterium NA
Seq68 Bacteria Actinobacteriota Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium NA
Seq293 Bacteria Actinobacteriota Actinobacteria Glycomycetales Glycomycetaceae Glycomyces NA
Seq72 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq101 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq265 Bacteria Actinobacteriota Actinobacteria Streptomycetales Streptomycetaceae Streptomyces NA
Seq260 Bacteria Bacteroidota Bacteroidia Sphingobacteriales NA NA NA
Seq180 Bacteria Bacteroidota Bacteroidia Sphingobacteriales Sphingobacteriaceae Pedobacter panaciterrae
Seq142 Bacteria Verrucomicrobiota Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Roseimicrobium NA
Seq163 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq253 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq116 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq184 Bacteria Bacteroidota Bacteroidia Cytophagales Microscillaceae Ohtaekwangia NA
Seq52 Bacteria Bacteroidota Bacteroidia Flavobacteriales Flavobacteriaceae Flavobacterium NA
Seq187 Bacteria Bacteroidota Bacteroidia Flavobacteriales Weeksellaceae Chryseobacterium ginsenosidimutans
Seq172 Bacteria Bacteroidota Bacteroidia Flavobacteriales Weeksellaceae Chryseobacterium NA
Seq283 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Flavitalea NA
Seq113 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq110 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Niastella NA
Seq132 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Pseudoflavitalea NA
Seq37 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq162 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq182 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga humicola
Seq92 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq80 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga pinensis
Seq2 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq221 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq20 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq282 Bacteria Bacteroidota Bacteroidia Chitinophagales Chitinophagaceae Chitinophaga NA
Seq38 Bacteria Bacteroidota Bacteroidia Cytophagales Spirosomaceae Dyadobacter NA
Seq237 Bacteria Proteobacteria Gammaproteobacteria Steroidobacterales Steroidobacteraceae Steroidobacter agariperforans
Seq234 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Pseudoxanthomonas NA
Seq59 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas NA
Seq105 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Stenotrophomonas NA
Seq344 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Lysobacter NA
Seq41 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Xanthomonadaceae Lysobacter NA
Seq243 Bacteria Proteobacteria Gammaproteobacteria NA NA NA NA
Seq406 Bacteria Proteobacteria Gammaproteobacteria Legionellales Legionellaceae Legionella NA
Seq139 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq24 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq27 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq87 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq55 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas NA
Seq201 Bacteria Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella NA

0.7 Add a metadata

IN_WORK!!

list.files("meta/")
## [1] "cell_realtime_stat.xlsx" "cell_resp_ch_stat.xlsx" 
## [3] "period_legend.xlsx"

period_legend - соответствие номеров мешочков в 16S с днями, думаю лучше заменить везде обозначения 1, 3 и тд на дни cell_resp - данные по дыханию, по ним какую-нибудь простую статистику. Да, повторностей для эксперимента и контроля разное количество cell_realtime - это циклы выхода целлюлаз по реалтайму, я их нормировала по 16S, есть в этой же таблице. Что с ними делать особо не знаю, вроде вообще решили выкинуть

realtime.data <- readxl::read_excel("meta/cell_realtime_stat.xlsx")
period.data <- readxl::read_excel("meta/period_legend.xlsx")
resp.data <- readxl::read_excel("meta/cell_resp_ch_stat.xlsx")
realtime.data
## # A tibble: 36 × 29
##    id        day contr…¹ CELL_…² CELL_…³ CELL_…⁴ CELL_…⁵ CELL_…⁶ CELL_…⁷ CELL_…⁸
##    <chr>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
##  1 G01-1-1     3    15.6    33.2    31.1    33.6    36.6    33.8    38.0    33.0
##  2 G01-1-2     3    15.5    33.3    31.3    32.9    36.2    33.8    41      32.7
##  3 G01-1-3     3    15.5    33.6    31.2    32.9    35.8    33.3    38.2    32.9
##  4 G01-2-1     3    17.1    36.0    31.1    33.1    36.9    36.4    38.8    33.8
##  5 G01-2-2     3    17.3    35.6    31.0    32.8    37.8    35.7    40.1    33.6
##  6 G01-2-3     3    17.1    36      31.1    32.8    38.1    35.2    37.6    33.6
##  7 G01-3-1     3    16.4    35.4    31.6    34.9    39.1    35.3    40.9    33.2
##  8 G01-3-2     3    16.5    35.6    31.3    34.4    37.9    34.6    38.9    33.1
##  9 G01-3-3     3    16.4    35.8    31.5    34.4    41.6    35.0    36.5    33.4
## 10 G05-1-1    28    18.2    26.3    29.1    29.4    28.2    28.4    37.4    34.5
## # … with 26 more rows, 19 more variables: CELL_193122 <dbl>, CELL_73229 <dbl>,
## #   CELL_47814 <dbl>, CELL_163125 <dbl>, CELL_73266 <dbl>, CELL_88582 <dbl>,
## #   CELL_63583 <dbl>, CELL_14199 <dbl>, CELL_95616 <dbl>, CELL_63504 <dbl>,
## #   CELL_08643 <chr>, CELL_199599 <dbl>, CELL_01426 <dbl>, CELL_71601 <dbl>,
## #   CELL_45099 <dbl>, CELL_191900 <dbl>, CELL_99463 <dbl>, CELL_74579 <dbl>,
## #   CELL_183403 <dbl>, and abbreviated variable names ¹​contr_16S, ²​CELL_172283,
## #   ³​CELL_203163, ⁴​CELL_83325, ⁵​CELL_188413, ⁶​CELL_109631, ⁷​CELL_188119, …
impute.mean <- function(x) replace(x, is.na(x), mean(x, na.rm = TRUE))

realtime_data <- realtime.data %>% 
  mutate(CELL_08643 = as.numeric(CELL_08643)) %>% 
  group_by(day) %>%
  mutate(nice_cell = impute.mean(CELL_08643)) %>% 
  mutate(day = as.factor(day))
## Warning in mask$eval_all_mutate(quo): NAs introduced by coercion
realtime_data
## # A tibble: 36 × 30
## # Groups:   day [4]
##    id      day   contr…¹ CELL_…² CELL_…³ CELL_…⁴ CELL_…⁵ CELL_…⁶ CELL_…⁷ CELL_…⁸
##    <chr>   <fct>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
##  1 G01-1-1 3        15.6    33.2    31.1    33.6    36.6    33.8    38.0    33.0
##  2 G01-1-2 3        15.5    33.3    31.3    32.9    36.2    33.8    41      32.7
##  3 G01-1-3 3        15.5    33.6    31.2    32.9    35.8    33.3    38.2    32.9
##  4 G01-2-1 3        17.1    36.0    31.1    33.1    36.9    36.4    38.8    33.8
##  5 G01-2-2 3        17.3    35.6    31.0    32.8    37.8    35.7    40.1    33.6
##  6 G01-2-3 3        17.1    36      31.1    32.8    38.1    35.2    37.6    33.6
##  7 G01-3-1 3        16.4    35.4    31.6    34.9    39.1    35.3    40.9    33.2
##  8 G01-3-2 3        16.5    35.6    31.3    34.4    37.9    34.6    38.9    33.1
##  9 G01-3-3 3        16.4    35.8    31.5    34.4    41.6    35.0    36.5    33.4
## 10 G05-1-1 28       18.2    26.3    29.1    29.4    28.2    28.4    37.4    34.5
## # … with 26 more rows, 20 more variables: CELL_193122 <dbl>, CELL_73229 <dbl>,
## #   CELL_47814 <dbl>, CELL_163125 <dbl>, CELL_73266 <dbl>, CELL_88582 <dbl>,
## #   CELL_63583 <dbl>, CELL_14199 <dbl>, CELL_95616 <dbl>, CELL_63504 <dbl>,
## #   CELL_08643 <dbl>, CELL_199599 <dbl>, CELL_01426 <dbl>, CELL_71601 <dbl>,
## #   CELL_45099 <dbl>, CELL_191900 <dbl>, CELL_99463 <dbl>, CELL_74579 <dbl>,
## #   CELL_183403 <dbl>, nice_cell <dbl>, and abbreviated variable names
## #   ¹​contr_16S, ²​CELL_172283, ³​CELL_203163, ⁴​CELL_83325, ⁵​CELL_188413, …
resp_data <- resp.data %>% 
  group_by(day) %>%
  mutate(control = impute.mean(control)) %>% 
  mutate(straw = impute.mean(straw)) 

resp_data
## # A tibble: 164 × 3
## # Groups:   day [27]
##      day control straw
##    <dbl>   <dbl> <dbl>
##  1     0    250   250 
##  2     3    285.  723.
##  3     3    263.  832.
##  4     3    131.  657.
##  5     3    307.  525.
##  6     3    241.  744.
##  7     3    245.  701.
##  8     3    245.  657.
##  9     7    274.  690.
## 10     7    296.  690.
## # … with 154 more rows

0.7.1 Knee plot

Дыхание - median(straw)/median(control)

Mожно использовать сторонний пакет(KneeArrower) что понять в каком месте knee_plot происходит перелом. Для элиминации повторностей возьмем медиану.   Я хз как этот пакет работает(ищет производную, но как сглаживает - хз, там матан), но он говорит что перелом происходит скорее на 60-80 днях.

(я исправил ошибки - стало ближе к твоим данным)

https://github.com/agentlans/KneeArrower - вот здесь можно почитать про матан

# resp_data %>% 
#   filter(!day == 0) %>% 
#   group_by(day) %>% 
#   summarise(median_control = median(control),
#             median_straw = median(straw)) %>% 
#   mutate(rel = median_straw/median_control) %>% 
#   ggplot() +
#   geom_point(aes(x = day, y = rel))

resp_median <- resp_data %>% 
  filter(!day == 0) %>% 
  group_by(day) %>% 
  summarise(median_control = median(control),
            median_straw = median(straw)) %>% 
  mutate(rel = median_straw/median_control)


thresholds <- c(0.25, 0.5, 0.75, 1)

# Find cutoff points at each threshold
cutoff.points <- lapply(thresholds, function(i) {
  findCutoff(resp_median$day, resp_median$rel, method="first", i)
})

x.coord <- sapply(cutoff.points, function(p) p$x)
y.coord <- sapply(cutoff.points, function(p) p$y)

# Plot the cutoff points on the scatterplot
plot(resp_median$day, resp_median$rel, pch=20, col="gray")
points(x.coord, y.coord, col="red", pch=20)
text(x.coord, y.coord, labels=thresholds, pos=4, col="red")

period.data
## # A tibble: 15 × 2
##    bag_id   day
##     <dbl> <dbl>
##  1      1     3
##  2      2     7
##  3      3    14
##  4      4    21
##  5      5    28
##  6      6    35
##  7      7    49
##  8      8    63
##  9      9    77
## 10     10    91
## 11     11   105
## 12     12   119
## 13     13   140
## 14     14   161
## 15     15   182

0.8 Export all phyloseq object in one table

IN_WORK!!!

В табличке есть колонка cluster - “exl” в ней обозначает что это та часть датасета которая не пошла в WGCNA - мажоры в единичных семплах.

ps.m <- phyloseq::psmelt(ps.f)

ps.m <- ps.m %>% 
  mutate_if(is.character, as.factor) 

ps.data.out <- ps.m %>%
  select(-Group) %>% 
  pivot_wider(names_from = c(Day, Description, Sample), values_from = Abundance, values_fill = 0) 

#create empty dataframe with columnnames
external_empty_dataframe <- data.frame(OTU=factor(), cluster=factor(), stringsAsFactors = FALSE)

for (i in names(l_vst)) {
  a <- taxa_names(l_vst[[i]][["ps"]])
  b <- rep(i, length(a))
  d <- data.frame(OTU = as.factor(a),
                  cluster = as.factor(b))
  external_empty_dataframe <- rbind(external_empty_dataframe, d)
}

clusters.otu.df <- external_empty_dataframe
# add exl taxa -- taxa "exl"
d <- data.frame(OTU = as.factor(ps.exl.taxa),
                cluster = as.factor(rep("exl", length(ps.exl.taxa))))

clusters.otu.df <- rbind(clusters.otu.df, d)
ps.data.out.exl <- left_join(clusters.otu.df, ps.data.out, by="OTU")
# write.table(ps.data.out.exl, file = "ps.data.out.tsv", sep = "\t")
ps.data.out.exl
##        OTU   cluster  Kingdom            Phylum               Class
## 1   Seq314      blue Bacteria     Cyanobacteria    Vampirivibrionia
## 2    Seq23      blue Bacteria     Cyanobacteria    Vampirivibrionia
## 3    Seq65      blue Bacteria    Proteobacteria Alphaproteobacteria
## 4   Seq188      blue Bacteria    Proteobacteria Alphaproteobacteria
## 5   Seq334      blue Bacteria    Proteobacteria Alphaproteobacteria
## 6    Seq75      blue Bacteria    Proteobacteria Alphaproteobacteria
## 7   Seq167      blue Bacteria    Proteobacteria Alphaproteobacteria
## 8   Seq273      blue Bacteria    Proteobacteria Alphaproteobacteria
## 9   Seq131      blue Bacteria    Proteobacteria Alphaproteobacteria
## 10  Seq138      blue Bacteria    Proteobacteria Alphaproteobacteria
## 11  Seq104      blue Bacteria    Proteobacteria Alphaproteobacteria
## 12  Seq129      blue Bacteria    Proteobacteria Alphaproteobacteria
## 13   Seq28      blue Bacteria    Proteobacteria Alphaproteobacteria
## 14  Seq360      blue Bacteria    Proteobacteria Alphaproteobacteria
## 15  Seq292      blue Bacteria    Proteobacteria Alphaproteobacteria
## 16  Seq166      blue Bacteria    Proteobacteria Alphaproteobacteria
## 17   Seq39      blue Bacteria   Gemmatimonadota    Gemmatimonadetes
## 18   Seq30      blue Bacteria  Actinobacteriota     Thermoleophilia
## 19  Seq151      blue Bacteria  Actinobacteriota     Thermoleophilia
## 20  Seq250      blue Bacteria  Actinobacteriota     Thermoleophilia
## 21  Seq135      blue Bacteria       Myxococcota           Polyangia
## 22   Seq46      blue Bacteria       Myxococcota           Polyangia
## 23   Seq35      blue Bacteria       Myxococcota           Polyangia
## 24  Seq106      blue Bacteria       Myxococcota           Polyangia
## 25  Seq345      blue Bacteria  Bdellovibrionota         Oligoflexia
## 26  Seq198      blue Bacteria  Bdellovibrionota     Bdellovibrionia
## 27   Seq97      blue Bacteria  Bdellovibrionota     Bdellovibrionia
## 28  Seq183      blue Bacteria      Dependentiae            Babeliae
## 29  Seq424      blue Bacteria  Actinobacteriota      Actinobacteria
## 30  Seq136      blue Bacteria  Actinobacteriota      Acidimicrobiia
## 31  Seq174      blue Bacteria  Actinobacteriota      Acidimicrobiia
## 32   Seq43      blue Bacteria  Actinobacteriota      Actinobacteria
## 33  Seq420      blue Bacteria  Actinobacteriota      Actinobacteria
## 34  Seq127      blue Bacteria  Actinobacteriota      Actinobacteria
## 35  Seq288      blue Bacteria  Actinobacteriota      Actinobacteria
## 36  Seq449      blue Bacteria  Actinobacteriota      Actinobacteria
## 37   Seq91      blue Bacteria      Bacteroidota         Bacteroidia
## 38  Seq149      blue Bacteria      Bacteroidota         Bacteroidia
## 39  Seq169      blue Bacteria      Bacteroidota         Bacteroidia
## 40   Seq81      blue Bacteria      Bacteroidota         Bacteroidia
## 41  Seq211      blue Bacteria      Bacteroidota         Bacteroidia
## 42  Seq119      blue Bacteria      Bacteroidota         Bacteroidia
## 43   Seq77      blue Bacteria     Spirochaetota        Spirochaetia
## 44  Seq175      blue Bacteria     Spirochaetota        Spirochaetia
## 45  Seq305      blue Bacteria       Chloroflexi        Anaerolineae
## 46  Seq379      blue Bacteria       Chloroflexi        Chloroflexia
## 47  Seq165      blue Bacteria       Chloroflexi        Chloroflexia
## 48  Seq327      blue Bacteria       Chloroflexi        Chloroflexia
## 49  Seq252      blue Bacteria    Armatimonadota      Fimbriimonadia
## 50  Seq382      blue Bacteria Verrucomicrobiota    Verrucomicrobiae
## 51  Seq123      blue Bacteria Verrucomicrobiota    Verrucomicrobiae
## 52  Seq124      blue Bacteria Verrucomicrobiota    Verrucomicrobiae
## 53  Seq325      blue Bacteria Verrucomicrobiota    Verrucomicrobiae
## 54  Seq272      blue Bacteria Verrucomicrobiota    Verrucomicrobiae
## 55  Seq402      blue Bacteria Verrucomicrobiota    Verrucomicrobiae
## 56  Seq322      blue Bacteria   Planctomycetota      Planctomycetes
## 57  Seq356      blue Bacteria   Planctomycetota      Planctomycetes
## 58  Seq259      blue Bacteria   Planctomycetota      Planctomycetes
## 59  Seq279      blue Bacteria   Planctomycetota      Planctomycetes
## 60  Seq214      blue Bacteria   Planctomycetota      Planctomycetes
## 61  Seq209      blue Bacteria   Planctomycetota      Planctomycetes
## 62  Seq229      blue Bacteria   Acidobacteriota    Vicinamibacteria
## 63  Seq275      blue Bacteria   Acidobacteriota    Vicinamibacteria
## 64  Seq247      blue Bacteria   Acidobacteriota    Vicinamibacteria
## 65  Seq316      blue Bacteria      Bacteroidota        Kapabacteria
## 66  Seq371      blue Bacteria      Bacteroidota         Bacteroidia
## 67   Seq12      blue Bacteria      Bacteroidota         Bacteroidia
## 68  Seq153      blue Bacteria      Bacteroidota         Bacteroidia
## 69  Seq326      blue Bacteria      Bacteroidota         Bacteroidia
## 70   Seq10      blue Bacteria      Bacteroidota         Bacteroidia
## 71   Seq82      blue Bacteria      Bacteroidota         Bacteroidia
## 72  Seq462      blue Bacteria      Bacteroidota         Bacteroidia
## 73  Seq150      blue Bacteria      Bacteroidota         Bacteroidia
## 74  Seq290      blue Bacteria      Bacteroidota         Bacteroidia
## 75  Seq339      blue Bacteria      Bacteroidota         Bacteroidia
## 76  Seq120      blue Bacteria      Bacteroidota         Bacteroidia
## 77  Seq233      blue Bacteria    Proteobacteria Gammaproteobacteria
## 78  Seq133      blue Bacteria    Proteobacteria Gammaproteobacteria
## 79  Seq349      blue Bacteria    Proteobacteria Gammaproteobacteria
## 80  Seq315      blue Bacteria    Proteobacteria Gammaproteobacteria
## 81   Seq57      blue Bacteria    Proteobacteria Gammaproteobacteria
## 82   Seq96      blue Bacteria    Proteobacteria Gammaproteobacteria
## 83  Seq170      blue Bacteria    Proteobacteria Gammaproteobacteria
## 84   Seq94      blue Bacteria    Proteobacteria Gammaproteobacteria
## 85  Seq114      blue Bacteria    Proteobacteria Gammaproteobacteria
## 86  Seq235      blue Bacteria    Proteobacteria Gammaproteobacteria
## 87   Seq98      cyan Bacteria    Proteobacteria Gammaproteobacteria
## 88   Seq64      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 89    Seq4      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 90  Seq244      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 91   Seq11      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 92   Seq74      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 93   Seq22      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 94   Seq45      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 95    Seq9      cyan Bacteria    Proteobacteria Alphaproteobacteria
## 96   Seq29      cyan Bacteria       Myxococcota           Polyangia
## 97  Seq239      cyan Bacteria       Myxococcota           Polyangia
## 98   Seq50      cyan Bacteria  Actinobacteriota      Actinobacteria
## 99   Seq34      cyan Bacteria  Actinobacteriota      Actinobacteria
## 100  Seq56      cyan Bacteria        Firmicutes             Bacilli
## 101  Seq25      cyan Bacteria        Firmicutes             Bacilli
## 102   Seq3      cyan Bacteria        Firmicutes             Bacilli
## 103   Seq5      cyan Bacteria        Firmicutes             Bacilli
## 104  Seq13      cyan Bacteria        Firmicutes             Bacilli
## 105   Seq7      cyan Bacteria        Firmicutes             Bacilli
## 106  Seq19      cyan Bacteria        Firmicutes             Bacilli
## 107  Seq17      cyan Bacteria   Planctomycetota      Planctomycetes
## 108 Seq324      cyan Bacteria   Acidobacteriota      Acidobacteriae
## 109  Seq16      cyan Bacteria      Bacteroidota         Bacteroidia
## 110   Seq6      cyan Bacteria      Bacteroidota         Bacteroidia
## 111   Seq1      cyan Bacteria      Bacteroidota         Bacteroidia
## 112 Seq109      cyan Bacteria      Bacteroidota         Bacteroidia
## 113  Seq49      cyan Bacteria      Bacteroidota         Bacteroidia
## 114  Seq73      cyan Bacteria      Bacteroidota         Bacteroidia
## 115  Seq15      cyan Bacteria    Proteobacteria Gammaproteobacteria
## 116  Seq26      cyan Bacteria    Proteobacteria Gammaproteobacteria
## 117 Seq342 darkgreen  Archaea     Crenarchaeota     Nitrososphaeria
## 118 Seq196 darkgreen  Archaea     Crenarchaeota     Nitrososphaeria
## 119 Seq276 darkgreen  Archaea     Crenarchaeota     Nitrososphaeria
## 120 Seq419 darkgreen  Archaea     Crenarchaeota     Nitrososphaeria
## 121 Seq454 darkgreen Bacteria    Proteobacteria Gammaproteobacteria
## 122 Seq329 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 123 Seq332 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 124 Seq429 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 125 Seq195 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 126 Seq144 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 127 Seq369 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 128 Seq362 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 129 Seq428 darkgreen Bacteria    Proteobacteria Alphaproteobacteria
## 130 Seq347 darkgreen Bacteria      Nitrospirota         Nitrospiria
## 131 Seq328 darkgreen Bacteria       Myxococcota           Polyangia
## 132 Seq348 darkgreen Bacteria       Myxococcota           Polyangia
## 133 Seq308 darkgreen Bacteria       Myxococcota           Polyangia
## 134 Seq256 darkgreen Bacteria       Myxococcota           Polyangia
## 135 Seq302 darkgreen Bacteria  Bdellovibrionota         Oligoflexia
## 136 Seq435 darkgreen Bacteria  Actinobacteriota      Actinobacteria
## 137 Seq291 darkgreen Bacteria  Actinobacteriota      Acidimicrobiia
## 138 Seq392 darkgreen Bacteria  Actinobacteriota      Acidimicrobiia
## 139 Seq321 darkgreen Bacteria      Bacteroidota         Bacteroidia
## 140 Seq186 darkgreen Bacteria        Firmicutes             Bacilli
## 141 Seq204 darkgreen Bacteria        Firmicutes             Bacilli
## 142 Seq146 darkgreen Bacteria     Spirochaetota        Spirochaetia
## 143 Seq359 darkgreen Bacteria   Patescibacteria     Saccharimonadia
## 144 Seq269 darkgreen Bacteria       Chloroflexi        Chloroflexia
## 145 Seq267 darkgreen Bacteria Verrucomicrobiota    Verrucomicrobiae
## 146 Seq320 darkgreen Bacteria Verrucomicrobiota    Verrucomicrobiae
## 147 Seq203 darkgreen Bacteria Verrucomicrobiota    Verrucomicrobiae
## 148 Seq497 darkgreen Bacteria   Planctomycetota      Planctomycetes
## 149 Seq384 darkgreen Bacteria   Planctomycetota      Planctomycetes
## 150 Seq155 darkgreen Bacteria   Acidobacteriota      Blastocatellia
## 151 Seq350 darkgreen Bacteria      Bacteroidota         Bacteroidia
## 152 Seq224 darkgreen Bacteria      Bacteroidota         Bacteroidia
## 153 Seq409 darkgreen Bacteria      Bacteroidota         Bacteroidia
## 154 Seq337 darkgreen Bacteria      Bacteroidota         Bacteroidia
## 155 Seq494 darkgreen Bacteria      Bacteroidota         Bacteroidia
## 156 Seq277 darkgreen Bacteria    Proteobacteria Gammaproteobacteria
## 157 Seq191 darkgreen Bacteria    Proteobacteria Gammaproteobacteria
## 158 Seq335 darkgreen Bacteria    Proteobacteria Gammaproteobacteria
## 159 Seq157 darkgreen Bacteria    Proteobacteria Gammaproteobacteria
## 160 Seq385 darkgreen Bacteria    Proteobacteria Gammaproteobacteria
## 161 Seq161      plum Bacteria    Proteobacteria Gammaproteobacteria
## 162 Seq181      plum Bacteria    Proteobacteria Gammaproteobacteria
## 163 Seq207      plum Bacteria     Cyanobacteria    Vampirivibrionia
## 164 Seq219      plum Bacteria    Proteobacteria Alphaproteobacteria
## 165 Seq216      plum Bacteria    Proteobacteria Alphaproteobacteria
## 166 Seq220      plum Bacteria    Proteobacteria Alphaproteobacteria
## 167  Seq90      plum Bacteria    Proteobacteria Alphaproteobacteria
## 168 Seq271      plum Bacteria    Proteobacteria Alphaproteobacteria
## 169 Seq111      plum Bacteria    Proteobacteria Alphaproteobacteria
## 170  Seq33      plum Bacteria    Proteobacteria Alphaproteobacteria
## 171 Seq189      plum Bacteria  Actinobacteriota     Thermoleophilia
## 172  Seq85      plum Bacteria       Myxococcota           Polyangia
## 173 Seq208      plum Bacteria  Actinobacteriota      Actinobacteria
## 174 Seq218      plum Bacteria      Bacteroidota         Bacteroidia
## 175 Seq215      plum Bacteria        Firmicutes             Bacilli
## 176 Seq177      plum Bacteria    Fibrobacterota       Fibrobacteria
## 177 Seq375      plum Bacteria       Chloroflexi        Chloroflexia
## 178 Seq430      plum Bacteria   Planctomycetota       Phycisphaerae
## 179 Seq368      plum Bacteria   Planctomycetota      Planctomycetes
## 180 Seq152      plum Bacteria   Planctomycetota      Planctomycetes
## 181 Seq304      plum Bacteria   Planctomycetota      Planctomycetes
## 182 Seq141      plum Bacteria      Bacteroidota         Bacteroidia
## 183 Seq343      plum Bacteria      Bacteroidota         Bacteroidia
## 184 Seq412      plum Bacteria      Bacteroidota         Bacteroidia
## 185 Seq457      plum Bacteria    Proteobacteria Gammaproteobacteria
## 186 Seq130      plum Bacteria    Proteobacteria Gammaproteobacteria
## 187 Seq346      plum Bacteria    Proteobacteria Gammaproteobacteria
## 188 Seq474      plum Bacteria    Proteobacteria Gammaproteobacteria
## 189 Seq472      plum Bacteria    Proteobacteria Gammaproteobacteria
## 190 Seq227      plum Bacteria    Proteobacteria Gammaproteobacteria
## 191 Seq117       red Bacteria    Proteobacteria Gammaproteobacteria
## 192  Seq60       red Bacteria    Proteobacteria Gammaproteobacteria
## 193 Seq121       red Bacteria    Proteobacteria Gammaproteobacteria
## 194 Seq383       red Bacteria    Proteobacteria Alphaproteobacteria
## 195 Seq228       red Bacteria    Proteobacteria Alphaproteobacteria
## 196 Seq178       red Bacteria    Proteobacteria Alphaproteobacteria
## 197 Seq171       red Bacteria    Proteobacteria Alphaproteobacteria
## 198 Seq341       red Bacteria    Proteobacteria Alphaproteobacteria
## 199  Seq89       red Bacteria    Proteobacteria Alphaproteobacteria
## 200  Seq31       red Bacteria    Proteobacteria Alphaproteobacteria
## 201 Seq160       red Bacteria    Proteobacteria Alphaproteobacteria
## 202 Seq251       red Bacteria    Proteobacteria Alphaproteobacteria
## 203 Seq373       red Bacteria    Proteobacteria Alphaproteobacteria
## 204 Seq108       red Bacteria    Proteobacteria Alphaproteobacteria
## 205  Seq71       red Bacteria  Actinobacteriota     Thermoleophilia
## 206 Seq338       red Bacteria       Myxococcota           Polyangia
## 207 Seq230       red Bacteria       Myxococcota           Polyangia
## 208  Seq88       red Bacteria       Myxococcota           Polyangia
## 209 Seq303       red Bacteria  Actinobacteriota      Acidimicrobiia
## 210  Seq93       red Bacteria  Actinobacteriota      Actinobacteria
## 211 Seq366       red Bacteria  Actinobacteriota      Actinobacteria
## 212 Seq134       red Bacteria  Actinobacteriota      Actinobacteria
## 213 Seq411       red Bacteria  Actinobacteriota      Actinobacteria
## 214 Seq115       red Bacteria  Actinobacteriota      Actinobacteria
## 215 Seq128       red Bacteria  Actinobacteriota      Actinobacteria
## 216 Seq398       red Bacteria  Actinobacteriota      Actinobacteria
## 217  Seq78       red Bacteria  Actinobacteriota      Actinobacteria
## 218 Seq193       red Bacteria  Actinobacteriota      Actinobacteria
## 219 Seq148       red Bacteria      Bacteroidota         Bacteroidia
## 220 Seq307       red Bacteria      Bacteroidota         Bacteroidia
## 221 Seq431       red Bacteria      Bacteroidota         Bacteroidia
## 222 Seq205       red Bacteria        Firmicutes             Bacilli
## 223  Seq86       red Bacteria        Firmicutes             Bacilli
## 224  Seq51       red Bacteria        Firmicutes             Bacilli
## 225  Seq18       red Bacteria        Firmicutes             Bacilli
## 226 Seq192       red Bacteria        Firmicutes             Bacilli
## 227 Seq266       red Bacteria        Firmicutes             Bacilli
## 228 Seq278       red Bacteria        Firmicutes             Bacilli
## 229  Seq99       red Bacteria        Firmicutes             Bacilli
## 230  Seq53       red Bacteria        Firmicutes             Bacilli
## 231 Seq118       red Bacteria        Firmicutes             Bacilli
## 232  Seq76       red Bacteria Verrucomicrobiota    Verrucomicrobiae
## 233 Seq232       red Bacteria Verrucomicrobiota    Verrucomicrobiae
## 234 Seq168       red Bacteria Verrucomicrobiota    Verrucomicrobiae
## 235 Seq387       red Bacteria Verrucomicrobiota    Verrucomicrobiae
## 236 Seq285       red Bacteria Verrucomicrobiota    Verrucomicrobiae
## 237 Seq217       red Bacteria Verrucomicrobiota    Verrucomicrobiae
## 238 Seq190       red Bacteria   Planctomycetota      Planctomycetes
## 239 Seq249       red Bacteria   Planctomycetota      Planctomycetes
## 240 Seq254       red Bacteria   Acidobacteriota      Acidobacteriae
## 241  Seq67       red Bacteria      Bacteroidota         Bacteroidia
## 242 Seq176       red Bacteria      Bacteroidota         Bacteroidia
## 243 Seq268       red Bacteria      Bacteroidota         Bacteroidia
## 244  Seq32       red Bacteria      Bacteroidota         Bacteroidia
## 245  Seq84       red Bacteria      Bacteroidota         Bacteroidia
## 246 Seq459       red Bacteria      Bacteroidota         Bacteroidia
## 247  Seq40       red Bacteria      Bacteroidota         Bacteroidia
## 248 Seq173       red Bacteria      Bacteroidota         Bacteroidia
## 249 Seq246       red Bacteria      Bacteroidota         Bacteroidia
## 250 Seq112       red Bacteria      Bacteroidota         Bacteroidia
## 251 Seq126       red Bacteria      Bacteroidota         Bacteroidia
## 252 Seq102       red Bacteria      Bacteroidota         Bacteroidia
## 253 Seq309       red Bacteria      Bacteroidota         Bacteroidia
## 254  Seq70       red Bacteria      Bacteroidota         Bacteroidia
## 255 Seq262       red Bacteria      Bacteroidota         Bacteroidia
## 256 Seq301       red Bacteria      Bacteroidota         Bacteroidia
## 257 Seq572       red Bacteria    Proteobacteria Gammaproteobacteria
## 258 Seq436       red Bacteria    Proteobacteria Gammaproteobacteria
## 259 Seq261       red Bacteria    Proteobacteria Gammaproteobacteria
## 260 Seq298       red Bacteria    Proteobacteria Gammaproteobacteria
## 261 Seq354       red Bacteria    Proteobacteria Gammaproteobacteria
## 262 Seq226       red Bacteria    Proteobacteria Gammaproteobacteria
## 263 Seq147       red Bacteria    Proteobacteria Gammaproteobacteria
## 264 Seq370       red Bacteria    Proteobacteria Gammaproteobacteria
## 265 Seq486       red Bacteria    Proteobacteria Gammaproteobacteria
## 266  Seq79    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 267 Seq122    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 268 Seq179    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 269 Seq145    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 270 Seq154    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 271 Seq222    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 272 Seq159    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 273   Seq8    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 274  Seq14    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 275  Seq54    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 276  Seq95    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 277 Seq340    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 278 Seq264    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 279 Seq333    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 280 Seq158    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 281 Seq248    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 282 Seq245    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 283 Seq185    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 284 Seq156    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 285  Seq42    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 286 Seq286    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 287  Seq21    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 288 Seq107    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 289 Seq231    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 290 Seq140    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 291 Seq378    salmon Bacteria    Proteobacteria Alphaproteobacteria
## 292 Seq374    salmon Bacteria       Myxococcota           Polyangia
## 293 Seq257    salmon Bacteria       Myxococcota           Polyangia
## 294 Seq223    salmon Bacteria  Actinobacteriota      Actinobacteria
## 295  Seq83    salmon Bacteria  Actinobacteriota      Actinobacteria
## 296  Seq68    salmon Bacteria  Actinobacteriota      Actinobacteria
## 297 Seq293    salmon Bacteria  Actinobacteriota      Actinobacteria
## 298  Seq72    salmon Bacteria  Actinobacteriota      Actinobacteria
## 299 Seq101    salmon Bacteria  Actinobacteriota      Actinobacteria
## 300 Seq265    salmon Bacteria  Actinobacteriota      Actinobacteria
## 301 Seq260    salmon Bacteria      Bacteroidota         Bacteroidia
## 302 Seq180    salmon Bacteria      Bacteroidota         Bacteroidia
## 303 Seq142    salmon Bacteria Verrucomicrobiota    Verrucomicrobiae
## 304 Seq163    salmon Bacteria      Bacteroidota         Bacteroidia
## 305 Seq253    salmon Bacteria      Bacteroidota         Bacteroidia
## 306 Seq116    salmon Bacteria      Bacteroidota         Bacteroidia
## 307 Seq184    salmon Bacteria      Bacteroidota         Bacteroidia
## 308  Seq52    salmon Bacteria      Bacteroidota         Bacteroidia
## 309 Seq187    salmon Bacteria      Bacteroidota         Bacteroidia
## 310 Seq172    salmon Bacteria      Bacteroidota         Bacteroidia
## 311 Seq283    salmon Bacteria      Bacteroidota         Bacteroidia
## 312 Seq113    salmon Bacteria      Bacteroidota         Bacteroidia
## 313 Seq110    salmon Bacteria      Bacteroidota         Bacteroidia
## 314 Seq132    salmon Bacteria      Bacteroidota         Bacteroidia
## 315  Seq37    salmon Bacteria      Bacteroidota         Bacteroidia
## 316 Seq162    salmon Bacteria      Bacteroidota         Bacteroidia
## 317 Seq182    salmon Bacteria      Bacteroidota         Bacteroidia
## 318  Seq92    salmon Bacteria      Bacteroidota         Bacteroidia
## 319  Seq80    salmon Bacteria      Bacteroidota         Bacteroidia
## 320   Seq2    salmon Bacteria      Bacteroidota         Bacteroidia
## 321 Seq221    salmon Bacteria      Bacteroidota         Bacteroidia
## 322  Seq20    salmon Bacteria      Bacteroidota         Bacteroidia
## 323 Seq282    salmon Bacteria      Bacteroidota         Bacteroidia
## 324  Seq38    salmon Bacteria      Bacteroidota         Bacteroidia
## 325 Seq237    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 326 Seq234    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 327  Seq59    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 328 Seq105    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 329 Seq344    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 330  Seq41    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 331 Seq243    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 332 Seq406    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 333 Seq139    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 334  Seq24    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 335  Seq27    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 336  Seq87    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 337  Seq55    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 338 Seq201    salmon Bacteria    Proteobacteria Gammaproteobacteria
## 339 Seq456       exl  Archaea     Crenarchaeota     Nitrososphaeria
## 340 Seq306       exl Bacteria    Proteobacteria Gammaproteobacteria
## 341 Seq423       exl Bacteria    Proteobacteria Gammaproteobacteria
## 342 Seq361       exl Bacteria    Proteobacteria Gammaproteobacteria
## 343 Seq416       exl Bacteria    Proteobacteria Gammaproteobacteria
## 344 Seq200       exl Bacteria    Proteobacteria Gammaproteobacteria
## 345 Seq427       exl Bacteria    Proteobacteria Gammaproteobacteria
## 346 Seq313       exl Bacteria    Proteobacteria Gammaproteobacteria
## 347 Seq432       exl Bacteria    Proteobacteria Gammaproteobacteria
## 348 Seq225       exl Bacteria    Proteobacteria Alphaproteobacteria
## 349 Seq380       exl Bacteria    Proteobacteria Alphaproteobacteria
## 350 Seq461       exl Bacteria    Proteobacteria Alphaproteobacteria
## 351 Seq440       exl Bacteria    Proteobacteria Alphaproteobacteria
## 352 Seq445       exl Bacteria    Proteobacteria Alphaproteobacteria
## 353 Seq357       exl Bacteria    Proteobacteria Alphaproteobacteria
## 354 Seq464       exl Bacteria    Proteobacteria                <NA>
## 355 Seq318       exl Bacteria    Proteobacteria Alphaproteobacteria
## 356 Seq397       exl Bacteria    Proteobacteria Alphaproteobacteria
## 357 Seq404       exl Bacteria    Proteobacteria Alphaproteobacteria
## 358 Seq310       exl Bacteria    Proteobacteria Alphaproteobacteria
## 359 Seq441       exl Bacteria    Proteobacteria Alphaproteobacteria
## 360 Seq311       exl Bacteria    Proteobacteria Alphaproteobacteria
## 361 Seq466       exl Bacteria    Proteobacteria Alphaproteobacteria
## 362 Seq468       exl Bacteria    Proteobacteria Alphaproteobacteria
## 363 Seq413       exl Bacteria    Proteobacteria Alphaproteobacteria
## 364 Seq443       exl Bacteria    Proteobacteria Alphaproteobacteria
## 365 Seq467       exl Bacteria    Proteobacteria Alphaproteobacteria
## 366 Seq395       exl Bacteria    Proteobacteria Alphaproteobacteria
## 367 Seq312       exl Bacteria    Proteobacteria Alphaproteobacteria
## 368 Seq439       exl Bacteria    Proteobacteria Alphaproteobacteria
## 369 Seq422       exl Bacteria   Gemmatimonadota    Gemmatimonadetes
## 370 Seq448       exl Bacteria  Actinobacteriota     Thermoleophilia
## 371 Seq284       exl Bacteria  Actinobacteriota     Thermoleophilia
## 372 Seq471       exl Bacteria  Actinobacteriota     Thermoleophilia
## 373 Seq391       exl Bacteria       Myxococcota          Myxococcia
## 374 Seq255       exl Bacteria       Myxococcota          Myxococcia
## 375 Seq442       exl Bacteria       Myxococcota          Myxococcia
## 376 Seq414       exl Bacteria       Myxococcota           Polyangia
## 377 Seq460       exl Bacteria  Bdellovibrionota     Bdellovibrionia
## 378 Seq418       exl Bacteria  Actinobacteriota      Actinobacteria
## 379 Seq447       exl Bacteria  Actinobacteriota      Actinobacteria
## 380 Seq450       exl Bacteria  Actinobacteriota      Actinobacteria
## 381 Seq238       exl Bacteria  Actinobacteriota      Acidimicrobiia
## 382 Seq289       exl Bacteria  Actinobacteriota      Actinobacteria
## 383 Seq394       exl Bacteria  Actinobacteriota      Actinobacteria
## 384 Seq401       exl Bacteria  Actinobacteriota      Actinobacteria
## 385 Seq455       exl Bacteria  Actinobacteriota      Actinobacteria
## 386 Seq451       exl Bacteria  Actinobacteriota      Actinobacteria
## 387 Seq363       exl Bacteria  Actinobacteriota      Actinobacteria
## 388 Seq358       exl Bacteria  Actinobacteriota      Actinobacteria
## 389 Seq294       exl Bacteria  Actinobacteriota      Actinobacteria
## 390 Seq297       exl Bacteria  Actinobacteriota      Actinobacteria
## 391 Seq415       exl Bacteria  Actinobacteriota      Actinobacteria
## 392 Seq469       exl Bacteria  Actinobacteriota      Actinobacteria
## 393 Seq400       exl Bacteria  Actinobacteriota      Actinobacteria
## 394 Seq212       exl Bacteria      Bacteroidota         Bacteroidia
## 395 Seq330       exl Bacteria      Bacteroidota         Bacteroidia
## 396 Seq444       exl Bacteria      Bacteroidota         Bacteroidia
## 397 Seq437       exl Bacteria      Bacteroidota         Bacteroidia
## 398 Seq453       exl Bacteria      Bacteroidota         Bacteroidia
## 399 Seq331       exl Bacteria      Bacteroidota         Bacteroidia
## 400 Seq143       exl Bacteria        Firmicutes             Bacilli
## 401  Seq69       exl Bacteria        Firmicutes             Bacilli
## 402 Seq296       exl Bacteria        Firmicutes             Bacilli
## 403 Seq280       exl Bacteria        Firmicutes             Bacilli
## 404 Seq426       exl Bacteria        Firmicutes             Bacilli
## 405 Seq365       exl Bacteria        Firmicutes             Bacilli
## 406 Seq452       exl Bacteria   Patescibacteria     Saccharimonadia
## 407 Seq336       exl Bacteria Verrucomicrobiota    Verrucomicrobiae
## 408 Seq376       exl Bacteria Verrucomicrobiota    Verrucomicrobiae
## 409 Seq364       exl Bacteria Verrucomicrobiota    Verrucomicrobiae
## 410 Seq202       exl Bacteria Verrucomicrobiota    Verrucomicrobiae
## 411 Seq367       exl Bacteria Verrucomicrobiota    Verrucomicrobiae
## 412 Seq263       exl Bacteria Verrucomicrobiota    Verrucomicrobiae
## 413 Seq446       exl Bacteria   Planctomycetota      Planctomycetes
## 414 Seq438       exl Bacteria   Planctomycetota      Planctomycetes
## 415 Seq425       exl Bacteria      Bacteroidota      Ignavibacteria
## 416 Seq295       exl Bacteria      Bacteroidota         Bacteroidia
## 417 Seq236       exl Bacteria      Bacteroidota         Bacteroidia
## 418 Seq299       exl Bacteria      Bacteroidota         Bacteroidia
## 419 Seq405       exl Bacteria      Bacteroidota         Bacteroidia
## 420 Seq410       exl Bacteria      Bacteroidota         Bacteroidia
## 421 Seq323       exl Bacteria      Bacteroidota         Bacteroidia
## 422 Seq199       exl Bacteria      Bacteroidota         Bacteroidia
## 423 Seq351       exl Bacteria      Bacteroidota         Bacteroidia
## 424 Seq407       exl Bacteria      Bacteroidota         Bacteroidia
## 425 Seq388       exl Bacteria      Bacteroidota         Bacteroidia
## 426 Seq396       exl Bacteria      Bacteroidota         Bacteroidia
## 427 Seq470       exl Bacteria      Bacteroidota         Bacteroidia
## 428 Seq274       exl Bacteria    Proteobacteria Gammaproteobacteria
## 429 Seq458       exl Bacteria    Proteobacteria Gammaproteobacteria
## 430 Seq242       exl Bacteria    Proteobacteria Gammaproteobacteria
## 431 Seq393       exl Bacteria    Proteobacteria Gammaproteobacteria
## 432 Seq463       exl Bacteria    Proteobacteria Gammaproteobacteria
## 433 Seq390       exl Bacteria    Proteobacteria Gammaproteobacteria
## 434 Seq417       exl Bacteria    Proteobacteria Gammaproteobacteria
## 435 Seq389       exl Bacteria    Proteobacteria Gammaproteobacteria
## 436 Seq403       exl Bacteria    Proteobacteria Gammaproteobacteria
## 437 Seq386       exl Bacteria    Proteobacteria Gammaproteobacteria
## 438 Seq377       exl Bacteria    Proteobacteria Gammaproteobacteria
## 439 Seq164       exl Bacteria    Proteobacteria Gammaproteobacteria
## 440  Seq66       exl Bacteria    Proteobacteria Gammaproteobacteria
## 441 Seq241       exl Bacteria    Proteobacteria Gammaproteobacteria
## 442 Seq434       exl Bacteria    Proteobacteria Gammaproteobacteria
## 443 Seq319       exl Bacteria    Proteobacteria Gammaproteobacteria
## 444 Seq125       exl Bacteria    Proteobacteria Gammaproteobacteria
## 445 Seq408       exl Bacteria    Proteobacteria Gammaproteobacteria
##                                  Order                         Family
## 1                    Obscuribacterales             Obscuribacteraceae
## 2                    Obscuribacterales             Obscuribacteraceae
## 3                     Sphingomonadales              Sphingomonadaceae
## 4                        Reyranellales                 Reyranellaceae
## 5                        Reyranellales                 Reyranellaceae
## 6                        Reyranellales                 Reyranellaceae
## 7                        Reyranellales                 Reyranellaceae
## 8                          Rhizobiales                    Kaistiaceae
## 9                          Rhizobiales              Xanthobacteraceae
## 10                       Micropepsales                 Micropepsaceae
## 11                       Micropepsales                 Micropepsaceae
## 12                    Sphingomonadales              Sphingomonadaceae
## 13                         Rhizobiales                    Devosiaceae
## 14                         Rhizobiales                   Rhizobiaceae
## 15                     Caulobacterales               Caulobacteraceae
## 16                     Caulobacterales                Hyphomonadaceae
## 17                    Gemmatimonadales              Gemmatimonadaceae
## 18                 Solirubrobacterales           Solirubrobacteraceae
## 19                 Solirubrobacterales                          67-14
## 20                 Solirubrobacterales                          67-14
## 21                        Polyangiales                        BIrii41
## 22                        Polyangiales                        BIrii41
## 23                        Polyangiales                        BIrii41
## 24                        Polyangiales                Sandaracinaceae
## 25                           0319-6G20                           <NA>
## 26                   Bdellovibrionales             Bdellovibrionaceae
## 27                   Bdellovibrionales             Bdellovibrionaceae
## 28                          Babeliales                       UBA12409
## 29                 Propionibacteriales                Nocardioidaceae
## 30                      Microtrichales                      Iamiaceae
## 31                      Microtrichales                      Iamiaceae
## 32                       Micrococcales              Microbacteriaceae
## 33                   Micromonosporales             Micromonosporaceae
## 34                   Micromonosporales             Micromonosporaceae
## 35                    Streptomycetales              Streptomycetaceae
## 36                 Propionibacteriales           Propionibacteriaceae
## 37                       Bacteroidales                           <NA>
## 38           Bacteroidetes VC2.1 Bac22                           <NA>
## 39                  Sphingobacteriales            Sphingobacteriaceae
## 40                  Sphingobacteriales           NS11-12 marine group
## 41                                <NA>                           <NA>
## 42                  Sphingobacteriales                     env.OPS 17
## 43                      Spirochaetales                Spirochaetaceae
## 44                      Spirochaetales                Spirochaetaceae
## 45                      Anaerolineales                Anaerolineaceae
## 46                      Chloroflexales                 Roseiflexaceae
## 47                      Chloroflexales                 Roseiflexaceae
## 48                   Thermomicrobiales                   JG30-KF-CM45
## 49                    Fimbriimonadales              Fimbriimonadaceae
## 50                      Pedosphaerales                Pedosphaeraceae
## 51                          Opitutales                    Opitutaceae
## 52                  Chthoniobacterales              Terrimicrobiaceae
## 53                  Chthoniobacterales            Chthoniobacteraceae
## 54                  Verrucomicrobiales            Verrucomicrobiaceae
## 55                  Verrucomicrobiales                 Rubritaleaceae
## 56                        Pirellulales                  Pirellulaceae
## 57                        Pirellulales                  Pirellulaceae
## 58                        Pirellulales                  Pirellulaceae
## 59                        Pirellulales                  Pirellulaceae
## 60                    Planctomycetales              Rubinisphaeraceae
## 61                    Planctomycetales                Schlesneriaceae
## 62                  Vicinamibacterales            Vicinamibacteraceae
## 63                  Vicinamibacterales            Vicinamibacteraceae
## 64                  Vicinamibacterales                           <NA>
## 65                     Kapabacteriales                           <NA>
## 66                        Cytophagales                Microscillaceae
## 67                        Cytophagales                Microscillaceae
## 68                        Cytophagales                Microscillaceae
## 69                        Cytophagales                Microscillaceae
## 70                        Cytophagales                Microscillaceae
## 71                     Chitinophagales               Chitinophagaceae
## 72                     Chitinophagales               Chitinophagaceae
## 73                     Chitinophagales               Chitinophagaceae
## 74                     Chitinophagales               Chitinophagaceae
## 75                     Chitinophagales               Chitinophagaceae
## 76                     Chitinophagales               Chitinophagaceae
## 77                     Pseudomonadales                        211ds20
## 78                  Steroidobacterales            Steroidobacteraceae
## 79                  Steroidobacterales            Steroidobacteraceae
## 80  Gammaproteobacteria Incertae Sedis                 Unknown Family
## 81  Gammaproteobacteria Incertae Sedis                 Unknown Family
## 82                               R7C24                           <NA>
## 83  Gammaproteobacteria Incertae Sedis                 Unknown Family
## 84                     Xanthomonadales             Rhodanobacteraceae
## 85                  Diplorickettsiales            Diplorickettsiaceae
## 86                       Legionellales                 Legionellaceae
## 87                     Burkholderiales               Burkholderiaceae
## 88                      Azospirillales                  Inquilinaceae
## 89                      Azospirillales                  Inquilinaceae
## 90                         Rhizobiales              Xanthobacteraceae
## 91                         Rhizobiales              Xanthobacteraceae
## 92                         Rhizobiales              Xanthobacteraceae
## 93                         Rhizobiales              Xanthobacteraceae
## 94                         Rhizobiales                   Rhizobiaceae
## 95                         Rhizobiales                   Rhizobiaceae
## 96                       Nannocystales                 Nannocystaceae
## 97                        Polyangiales                  Polyangiaceae
## 98                   Corynebacteriales               Mycobacteriaceae
## 99                 Streptosporangiales           Streptosporangiaceae
## 100                    Paenibacillales               Paenibacillaceae
## 101                         Bacillales                    Bacillaceae
## 102                         Bacillales                    Bacillaceae
## 103                         Bacillales                    Bacillaceae
## 104                         Bacillales                 Planococcaceae
## 105                         Bacillales                 Planococcaceae
## 106                         Bacillales                 Planococcaceae
## 107                      Isosphaerales                 Isosphaeraceae
## 108                   Acidobacteriales Acidobacteriaceae (Subgroup 1)
## 109                       Cytophagales                Microscillaceae
## 110                       Cytophagales                Microscillaceae
## 111                    Chitinophagales               Chitinophagaceae
## 112                    Chitinophagales               Chitinophagaceae
## 113                    Chitinophagales               Chitinophagaceae
## 114                       Cytophagales                  Spirosomaceae
## 115                    Xanthomonadales             Rhodanobacteraceae
## 116                    Xanthomonadales               Xanthomonadaceae
## 117                  Nitrososphaerales             Nitrososphaeraceae
## 118                  Nitrososphaerales             Nitrososphaeraceae
## 119                  Nitrososphaerales             Nitrososphaeraceae
## 120                  Nitrososphaerales             Nitrososphaeraceae
## 121                 Diplorickettsiales            Diplorickettsiaceae
## 122                   Sphingomonadales              Sphingomonadaceae
## 123                   Rhodospirillales               Magnetospiraceae
## 124                    Acetobacterales               Acetobacteraceae
## 125                        Rhizobiales              Xanthobacteraceae
## 126                        Rhizobiales              Xanthobacteraceae
## 127                      Micropepsales                 Micropepsaceae
## 128                   Sphingomonadales              Sphingomonadaceae
## 129                    Caulobacterales               Caulobacteraceae
## 130                      Nitrospirales                 Nitrospiraceae
## 131                       Haliangiales                  Haliangiaceae
## 132                       Polyangiales                        BIrii41
## 133                       Polyangiales                        BIrii41
## 134                       Polyangiales                  Polyangiaceae
## 135                          0319-6G20                           <NA>
## 136                Propionibacteriales           Propionibacteriaceae
## 137                          IMCC26256                           <NA>
## 138                     Microtrichales             Ilumatobacteraceae
## 139                 Sphingobacteriales           NS11-12 marine group
## 140                    Paenibacillales               Paenibacillaceae
## 141                         Bacillales                 Planococcaceae
## 142                     Spirochaetales                Spirochaetaceae
## 143                  Saccharimonadales                           LWQ8
## 144                     Chloroflexales                 Roseiflexaceae
## 145                         Opitutales                    Opitutaceae
## 146                         Opitutales                    Opitutaceae
## 147                 Chthoniobacterales              Terrimicrobiaceae
## 148                       Pirellulales                  Pirellulaceae
## 149                   Planctomycetales                           <NA>
## 150                   Blastocatellales              Blastocatellaceae
## 151                 Sphingobacteriales                     env.OPS 17
## 152                    Chitinophagales               Chitinophagaceae
## 153                    Chitinophagales               Chitinophagaceae
## 154                    Chitinophagales               Chitinophagaceae
## 155                       Cytophagales                Amoebophilaceae
## 156                               <NA>                           <NA>
## 157 Gammaproteobacteria Incertae Sedis                 Unknown Family
## 158                    Xanthomonadales               Xanthomonadaceae
## 159                    Xanthomonadales             Rhodanobacteraceae
## 160                   Salinisphaerales                 Solimonadaceae
## 161                 Diplorickettsiales            Diplorickettsiaceae
## 162                              CCD24                           <NA>
## 163                  Obscuribacterales             Obscuribacteraceae
## 164                   Sphingomonadales              Sphingomonadaceae
## 165                          Dongiales                     Dongiaceae
## 166                      Reyranellales                 Reyranellaceae
## 167                        Rhizobiales              Xanthobacteraceae
## 168                        Rhizobiales              Xanthobacteraceae
## 169                   Sphingomonadales              Sphingomonadaceae
## 170                    Caulobacterales               Caulobacteraceae
## 171                Solirubrobacterales           Solirubrobacteraceae
## 172                       Polyangiales                        BIrii41
## 173                      Micrococcales              Microbacteriaceae
## 174                 Sphingobacteriales            Sphingobacteriaceae
## 175                         Bacillales                    Bacillaceae
## 176                    Fibrobacterales               Fibrobacteraceae
## 177                  Thermomicrobiales                   JG30-KF-CM45
## 178                    Phycisphaerales               Phycisphaeraceae
## 179                       Pirellulales                  Pirellulaceae
## 180                         Gemmatales                    Gemmataceae
## 181                   Planctomycetales                           <NA>
## 182                    Chitinophagales               Chitinophagaceae
## 183                    Chitinophagales               Chitinophagaceae
## 184                    Chitinophagales               Chitinophagaceae
## 185                        Coxiellales                   Coxiellaceae
## 186                              R7C24                           <NA>
## 187                   Salinisphaerales                 Solimonadaceae
## 188                 Diplorickettsiales            Diplorickettsiaceae
## 189                 Diplorickettsiales            Diplorickettsiaceae
## 190                 Diplorickettsiales            Diplorickettsiaceae
## 191                    Burkholderiales               Burkholderiaceae
## 192                    Burkholderiales                 Alcaligenaceae
## 193                    Burkholderiales                 Comamonadaceae
## 194                   Ferrovibrionales              Ferrovibrionaceae
## 195                        Rhizobiales              Xanthobacteraceae
## 196                        Rhizobiales               Beijerinckiaceae
## 197                        Rhizobiales               Beijerinckiaceae
## 198                        Rhizobiales               Beijerinckiaceae
## 199                        Rhizobiales              Xanthobacteraceae
## 200                        Rhizobiales              Xanthobacteraceae
## 201                        Rhizobiales              Hyphomicrobiaceae
## 202                   Sphingomonadales              Sphingomonadaceae
## 203                   Sphingomonadales              Sphingomonadaceae
## 204                        Rhizobiales                   Rhizobiaceae
## 205                Solirubrobacterales           Solirubrobacteraceae
## 206                       Polyangiales                  Polyangiaceae
## 207                       Polyangiales                  Polyangiaceae
## 208                       Polyangiales                  Polyangiaceae
## 209                     Microtrichales             Ilumatobacteraceae
## 210                      Micrococcales          Promicromonosporaceae
## 211                      Micrococcales              Microbacteriaceae
## 212                      Micrococcales              Microbacteriaceae
## 213                      Micrococcales              Microbacteriaceae
## 214                  Corynebacteriales               Mycobacteriaceae
## 215                Streptosporangiales           Streptosporangiaceae
## 216                Streptosporangiales           Streptosporangiaceae
## 217                Streptosporangiales            Thermomonosporaceae
## 218                   Streptomycetales              Streptomycetaceae
## 219                 Sphingobacteriales            Sphingobacteriaceae
## 220                 Sphingobacteriales           NS11-12 marine group
## 221                 Sphingobacteriales           NS11-12 marine group
## 222                    Paenibacillales               Paenibacillaceae
## 223                    Paenibacillales               Paenibacillaceae
## 224                    Paenibacillales               Paenibacillaceae
## 225                    Paenibacillales               Paenibacillaceae
## 226                    Paenibacillales               Paenibacillaceae
## 227                    Paenibacillales               Paenibacillaceae
## 228                         Bacillales                 Planococcaceae
## 229                         Bacillales                    Bacillaceae
## 230                         Bacillales                 Planococcaceae
## 231                         Bacillales                 Planococcaceae
## 232                 Chthoniobacterales              Terrimicrobiaceae
## 233                 Chthoniobacterales              Terrimicrobiaceae
## 234                 Chthoniobacterales              Terrimicrobiaceae
## 235                 Chthoniobacterales            Chthoniobacteraceae
## 236                 Chthoniobacterales            Chthoniobacteraceae
## 237                 Verrucomicrobiales            Verrucomicrobiaceae
## 238                         Gemmatales                    Gemmataceae
## 239                      Isosphaerales                 Isosphaeraceae
## 240                   Acidobacteriales Acidobacteriaceae (Subgroup 1)
## 241                       Cytophagales                Microscillaceae
## 242                       Cytophagales                Microscillaceae
## 243                    Chitinophagales               Chitinophagaceae
## 244                    Chitinophagales               Chitinophagaceae
## 245                    Chitinophagales               Chitinophagaceae
## 246                    Chitinophagales               Chitinophagaceae
## 247                    Chitinophagales               Chitinophagaceae
## 248                    Chitinophagales               Chitinophagaceae
## 249                    Chitinophagales               Chitinophagaceae
## 250                    Chitinophagales               Chitinophagaceae
## 251                    Chitinophagales               Chitinophagaceae
## 252                    Chitinophagales               Chitinophagaceae
## 253                    Chitinophagales               Chitinophagaceae
## 254                    Chitinophagales               Chitinophagaceae
## 255                    Chitinophagales               Chitinophagaceae
## 256                    Chitinophagales               Chitinophagaceae
## 257                    Pseudomonadales                  Moraxellaceae
## 258                 Steroidobacterales            Steroidobacteraceae
## 259 Gammaproteobacteria Incertae Sedis                 Unknown Family
## 260 Gammaproteobacteria Incertae Sedis                 Unknown Family
## 261 Gammaproteobacteria Incertae Sedis                 Unknown Family
## 262                    Xanthomonadales             Rhodanobacteraceae
## 263                    Xanthomonadales               Xanthomonadaceae
## 264                 Diplorickettsiales            Diplorickettsiaceae
## 265                               <NA>                           <NA>
## 266                    Burkholderiales               Oxalobacteraceae
## 267                    Burkholderiales               Oxalobacteraceae
## 268                    Burkholderiales               Oxalobacteraceae
## 269                    Burkholderiales               Oxalobacteraceae
## 270                    Burkholderiales               Oxalobacteraceae
## 271                    Burkholderiales               Oxalobacteraceae
## 272                    Burkholderiales               Burkholderiaceae
## 273                    Burkholderiales               Burkholderiaceae
## 274                    Burkholderiales                 Alcaligenaceae
## 275                    Burkholderiales                 Comamonadaceae
## 276                    Burkholderiales                 Comamonadaceae
## 277                    Burkholderiales                 Comamonadaceae
## 278                   Sphingomonadales              Sphingomonadaceae
## 279                      Reyranellales                 Reyranellaceae
## 280                        Rhizobiales               Beijerinckiaceae
## 281                        Rhizobiales                   Rhizobiaceae
## 282                        Rhizobiales                    Devosiaceae
## 283                        Rhizobiales                   Rhizobiaceae
## 284                        Rhizobiales                   Rhizobiaceae
## 285                        Rhizobiales                   Rhizobiaceae
## 286                        Rhizobiales                   Rhizobiaceae
## 287                        Rhizobiales                   Rhizobiaceae
## 288                        Rhizobiales                   Rhizobiaceae
## 289                        Rhizobiales                   Rhizobiaceae
## 290                        Rhizobiales                   Rhizobiaceae
## 291                    Caulobacterales               Caulobacteraceae
## 292                       Haliangiales                  Haliangiaceae
## 293                       Polyangiales                  Polyangiaceae
## 294                      Micrococcales          Promicromonosporaceae
## 295                      Micrococcales              Microbacteriaceae
## 296                  Corynebacteriales               Mycobacteriaceae
## 297                     Glycomycetales                Glycomycetaceae
## 298                   Streptomycetales              Streptomycetaceae
## 299                   Streptomycetales              Streptomycetaceae
## 300                   Streptomycetales              Streptomycetaceae
## 301                 Sphingobacteriales                           <NA>
## 302                 Sphingobacteriales            Sphingobacteriaceae
## 303                 Verrucomicrobiales            Verrucomicrobiaceae
## 304                       Cytophagales                Microscillaceae
## 305                       Cytophagales                Microscillaceae
## 306                       Cytophagales                Microscillaceae
## 307                       Cytophagales                Microscillaceae
## 308                   Flavobacteriales              Flavobacteriaceae
## 309                   Flavobacteriales                  Weeksellaceae
## 310                   Flavobacteriales                  Weeksellaceae
## 311                    Chitinophagales               Chitinophagaceae
## 312                    Chitinophagales               Chitinophagaceae
## 313                    Chitinophagales               Chitinophagaceae
## 314                    Chitinophagales               Chitinophagaceae
## 315                    Chitinophagales               Chitinophagaceae
## 316                    Chitinophagales               Chitinophagaceae
## 317                    Chitinophagales               Chitinophagaceae
## 318                    Chitinophagales               Chitinophagaceae
## 319                    Chitinophagales               Chitinophagaceae
## 320                    Chitinophagales               Chitinophagaceae
## 321                    Chitinophagales               Chitinophagaceae
## 322                    Chitinophagales               Chitinophagaceae
## 323                    Chitinophagales               Chitinophagaceae
## 324                       Cytophagales                  Spirosomaceae
## 325                 Steroidobacterales            Steroidobacteraceae
## 326                    Xanthomonadales               Xanthomonadaceae
## 327                    Xanthomonadales               Xanthomonadaceae
## 328                    Xanthomonadales               Xanthomonadaceae
## 329                    Xanthomonadales               Xanthomonadaceae
## 330                    Xanthomonadales               Xanthomonadaceae
## 331                               <NA>                           <NA>
## 332                      Legionellales                 Legionellaceae
## 333                    Pseudomonadales               Pseudomonadaceae
## 334                    Pseudomonadales               Pseudomonadaceae
## 335                    Pseudomonadales               Pseudomonadaceae
## 336                    Pseudomonadales               Pseudomonadaceae
## 337                    Pseudomonadales               Pseudomonadaceae
## 338                   Enterobacterales             Enterobacteriaceae
## 339                  Nitrososphaerales             Nitrososphaeraceae
## 340                    Burkholderiales               Oxalobacteraceae
## 341                    Burkholderiales                  Neisseriaceae
## 342                    Burkholderiales               Burkholderiaceae
## 343                    Burkholderiales               Burkholderiaceae
## 344                    Burkholderiales                 Alcaligenaceae
## 345                    Burkholderiales                 Alcaligenaceae
## 346                    Burkholderiales                 Alcaligenaceae
## 347                    Burkholderiales                 Comamonadaceae
## 348                   Sphingomonadales              Sphingomonadaceae
## 349                   Sphingomonadales              Sphingomonadaceae
## 350                   Sphingomonadales              Sphingomonadaceae
## 351                   Ferrovibrionales              Ferrovibrionaceae
## 352                      Reyranellales                 Reyranellaceae
## 353                      Reyranellales                 Reyranellaceae
## 354                               <NA>                           <NA>
## 355                        Rhizobiales                    Kaistiaceae
## 356                        Rhizobiales              Xanthobacteraceae
## 357                        Rhizobiales               Beijerinckiaceae
## 358                        Rhizobiales               Beijerinckiaceae
## 359                        Rhizobiales              Xanthobacteraceae
## 360                        Rhizobiales              Xanthobacteraceae
## 361                        Rhizobiales              Xanthobacteraceae
## 362                        Rhizobiales              Hyphomicrobiaceae
## 363                   Sphingomonadales              Sphingomonadaceae
## 364                        Rhizobiales                    Devosiaceae
## 365                        Rhizobiales                   Rhizobiaceae
## 366                        Rhizobiales                          D05-2
## 367                    Caulobacterales               Caulobacteraceae
## 368                    Caulobacterales               Caulobacteraceae
## 369                   Gemmatimonadales              Gemmatimonadaceae
## 370                         Gaiellales                           <NA>
## 371                Solirubrobacterales           Solirubrobacteraceae
## 372                Solirubrobacterales                          67-14
## 373                       Myxococcales                  Myxococcaceae
## 374                       Myxococcales                  Myxococcaceae
## 375                       Myxococcales                  Myxococcaceae
## 376                       Polyangiales             Phaselicystidaceae
## 377                  Bdellovibrionales             Bdellovibrionaceae
## 378                Propionibacteriales           Propionibacteriaceae
## 379                Propionibacteriales                Nocardioidaceae
## 380                Propionibacteriales                Nocardioidaceae
## 381                     Microtrichales                      Iamiaceae
## 382                      Micrococcales              Cellulomonadaceae
## 383                      Micrococcales              Cellulomonadaceae
## 384                      Micrococcales              Microbacteriaceae
## 385                      Micrococcales              Microbacteriaceae
## 386                  Micromonosporales             Micromonosporaceae
## 387                  Micromonosporales             Micromonosporaceae
## 388                  Micromonosporales             Micromonosporaceae
## 389                  Pseudonocardiales             Pseudonocardiaceae
## 390                Streptosporangiales           Streptosporangiaceae
## 391                   Streptomycetales              Streptomycetaceae
## 392                   Streptomycetales              Streptomycetaceae
## 393                         Frankiales                           <NA>
## 394                 Sphingobacteriales            Sphingobacteriaceae
## 395                 Sphingobacteriales            Sphingobacteriaceae
## 396                 Sphingobacteriales            Sphingobacteriaceae
## 397                 Sphingobacteriales            Sphingobacteriaceae
## 398                       Cytophagales                Microscillaceae
## 399                 Sphingobacteriales                     env.OPS 17
## 400                    Lactobacillales               Lactobacillaceae
## 401                    Lactobacillales               Lactobacillaceae
## 402                    Lactobacillales               Lactobacillaceae
## 403                    Lactobacillales               Lactobacillaceae
## 404                    Paenibacillales               Paenibacillaceae
## 405                         Bacillales                 Planococcaceae
## 406                  Saccharimonadales                           <NA>
## 407                 Chthoniobacterales              Terrimicrobiaceae
## 408                 Chthoniobacterales              Terrimicrobiaceae
## 409                 Chthoniobacterales              Terrimicrobiaceae
## 410                 Chthoniobacterales              Terrimicrobiaceae
## 411                 Chthoniobacterales              Terrimicrobiaceae
## 412                 Verrucomicrobiales                 Rubritaleaceae
## 413                       Pirellulales                  Pirellulaceae
## 414                       Pirellulales                  Pirellulaceae
## 415                             SJA-28                           <NA>
## 416                       Cytophagales                Microscillaceae
## 417                       Cytophagales                Microscillaceae
## 418                       Cytophagales                Microscillaceae
## 419                       Cytophagales                Microscillaceae
## 420                    Chitinophagales               Chitinophagaceae
## 421                    Chitinophagales               Chitinophagaceae
## 422                    Chitinophagales               Chitinophagaceae
## 423                    Chitinophagales               Chitinophagaceae
## 424                    Chitinophagales               Chitinophagaceae
## 425                    Chitinophagales               Chitinophagaceae
## 426                       Cytophagales                Microscillaceae
## 427                       Cytophagales                  Spirosomaceae
## 428                              CCD24                           <NA>
## 429                 Diplorickettsiales            Diplorickettsiaceae
## 430 Gammaproteobacteria Incertae Sedis                 Unknown Family
## 431                              R7C24                           <NA>
## 432                    Xanthomonadales               Xanthomonadaceae
## 433                    Xanthomonadales               Xanthomonadaceae
## 434                    Xanthomonadales               Xanthomonadaceae
## 435                    Xanthomonadales             Rhodanobacteraceae
## 436                    Xanthomonadales             Rhodanobacteraceae
## 437                        Coxiellales                   Coxiellaceae
## 438                 Diplorickettsiales            Diplorickettsiaceae
## 439                    Pseudomonadales               Pseudomonadaceae
## 440                    Pseudomonadales               Pseudomonadaceae
## 441                    Pseudomonadales               Pseudomonadaceae
## 442                    Pseudomonadales               Pseudomonadaceae
## 443                    Pseudomonadales               Pseudomonadaceae
## 444                   Enterobacterales             Enterobacteriaceae
## 445                   Enterobacterales                    Erwiniaceae
##                                                  Genus           Species
## 1                                                 <NA>              <NA>
## 2                                                 <NA>              <NA>
## 3                                         Sphingomonas              <NA>
## 4                                           Reyranella              soli
## 5                                           Reyranella              <NA>
## 6                                           Reyranella              <NA>
## 7                                           Reyranella      massiliensis
## 8                                              Kaistia              <NA>
## 9                                         Pseudolabrys              <NA>
## 10                                                <NA>              <NA>
## 11                                                <NA>              <NA>
## 12                                  Altererythrobacter              <NA>
## 13                                             Devosia              <NA>
## 14                                       Mesorhizobium              <NA>
## 15                                                <NA>              <NA>
## 16                                            Hirschia              <NA>
## 17                                                <NA>              <NA>
## 18                                        Conexibacter              <NA>
## 19                                                <NA>              <NA>
## 20                                                <NA>              <NA>
## 21                                                <NA>              <NA>
## 22                                                <NA>              <NA>
## 23                                                <NA>              <NA>
## 24                                                <NA>              <NA>
## 25                                                <NA>              <NA>
## 26                                        Bdellovibrio              <NA>
## 27                                        Bdellovibrio              <NA>
## 28                                                <NA>              <NA>
## 29                                           Kribbella              <NA>
## 30                                               Iamia              <NA>
## 31                                               Iamia              <NA>
## 32                                          Galbitalea              <NA>
## 33                                       Luedemannella              <NA>
## 34                                   Dactylosporangium              <NA>
## 35                                                <NA>              <NA>
## 36                                           Jiangella              <NA>
## 37                                                <NA>              <NA>
## 38                                                <NA>              <NA>
## 39                                    Mucilaginibacter       calamicampi
## 40                                                <NA>              <NA>
## 41                                                <NA>              <NA>
## 42                                                <NA>              <NA>
## 43                                         Salinispira              <NA>
## 44                                       Spirochaeta 2              <NA>
## 45                                                <NA>              <NA>
## 46                                                <NA>              <NA>
## 47                                                <NA>              <NA>
## 48                                                <NA>              <NA>
## 49                                                <NA>              <NA>
## 50                                                <NA>              <NA>
## 51                                       Lacunisphaera        limnophila
## 52                                      Terrimicrobium              <NA>
## 53                                                LD29              <NA>
## 54                                      Roseimicrobium    gellanilyticum
## 55                                       Luteolibacter              <NA>
## 56                                                <NA>              <NA>
## 57                                                <NA>              <NA>
## 58                                        Pir4 lineage              <NA>
## 59                                        Pir4 lineage              <NA>
## 60                                             SH-PL14              <NA>
## 61                                         Schlesneria              <NA>
## 62                                                <NA>              <NA>
## 63                                                <NA>              <NA>
## 64                                                <NA>              <NA>
## 65                                                <NA>              <NA>
## 66                                        Ohtaekwangia              <NA>
## 67                                        Ohtaekwangia              <NA>
## 68                                        Ohtaekwangia              <NA>
## 69                                        Ohtaekwangia              <NA>
## 70                                                <NA>              <NA>
## 71                                          Terrimonas              <NA>
## 72                                    Pseudoflavitalea              <NA>
## 73                                          Flavitalea              <NA>
## 74                                       Edaphobaculum              <NA>
## 75                                       Edaphobaculum              <NA>
## 76                                          Taibaiella              <NA>
## 77                                                <NA>              <NA>
## 78                                      Steroidobacter            flavus
## 79                                      Steroidobacter              <NA>
## 80                                         Acidibacter              <NA>
## 81                                         Acidibacter              <NA>
## 82                                                <NA>              <NA>
## 83                                         Acidibacter              <NA>
## 84                                          Dokdonella      ginsengisoli
## 85                                                <NA>              <NA>
## 86                                          Legionella              <NA>
## 87          Burkholderia-Caballeronia-Paraburkholderia          telluris
## 88                                          Inquilinus      ginsengisoli
## 89                                          Inquilinus              <NA>
## 90                                   Pseudorhodoplanes              <NA>
## 91                                      Bradyrhizobium              <NA>
## 92                                      Bradyrhizobium              <NA>
## 93                                            Starkeya              <NA>
## 94  Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium              <NA>
## 95  Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium              <NA>
## 96                                         Nannocystis              <NA>
## 97                                         Labilithrix              <NA>
## 98                                       Mycobacterium              <NA>
## 99                                        Herbidospora              <NA>
## 100                                      Paenibacillus              <NA>
## 101                                      Terribacillus              <NA>
## 102                                           Bacillus              <NA>
## 103                                           Bacillus              <NA>
## 104                                               <NA>              <NA>
## 105                                       Solibacillus              <NA>
## 106                                       Solibacillus              <NA>
## 107                                     Singulisphaera              <NA>
## 108                                       Edaphobacter              <NA>
## 109                                       Ohtaekwangia              <NA>
## 110                                       Ohtaekwangia              <NA>
## 111                                       Chitinophaga              <NA>
## 112                                       Chitinophaga              <NA>
## 113                                         Taibaiella              <NA>
## 114                                        Dyadobacter              <NA>
## 115                                        Luteibacter              <NA>
## 116                                         Luteimonas              <NA>
## 117                                               <NA>              <NA>
## 118                           Candidatus Nitrocosmicus              <NA>
## 119                                               <NA>              <NA>
## 120                                               <NA>              <NA>
## 121                                          Aquicella              <NA>
## 122                                       Sphingomonas            jaspsi
## 123                                               <NA>              <NA>
## 124                                               <NA>              <NA>
## 125                                  Pseudorhodoplanes              <NA>
## 126                                       Pseudolabrys              <NA>
## 127                                               <NA>              <NA>
## 128                                 Altererythrobacter              <NA>
## 129                                   Phenylobacterium              <NA>
## 130                                         Nitrospira          japonica
## 131                                         Haliangium              <NA>
## 132                                               <NA>              <NA>
## 133                                               <NA>              <NA>
## 134                                         Minicystis              <NA>
## 135                                               <NA>              <NA>
## 136                                       Microlunatus              <NA>
## 137                                               <NA>              <NA>
## 138                                               <NA>              <NA>
## 139                                               <NA>              <NA>
## 140                                      Paenibacillus              <NA>
## 141                                  Paenisporosarcina              <NA>
## 142                                      Spirochaeta 2              <NA>
## 143                                               <NA>              <NA>
## 144                                               <NA>              <NA>
## 145                                      Lacunisphaera              <NA>
## 146                                           Opitutus              <NA>
## 147                                     Terrimicrobium              <NA>
## 148                                               <NA>              <NA>
## 149                                               <NA>              <NA>
## 150                                               <NA>              <NA>
## 151                                               <NA>              <NA>
## 152                                         Terrimonas              <NA>
## 153                                      Edaphobaculum              <NA>
## 154                                         Taibaiella              <NA>
## 155                            Candidatus Amoebophilus              <NA>
## 156                                               <NA>              <NA>
## 157                                        Acidibacter              <NA>
## 158                                         Luteimonas            vadosa
## 159                                         Dokdonella              <NA>
## 160                                               <NA>              <NA>
## 161                                          Aquicella              <NA>
## 162                                               <NA>              <NA>
## 163                                               <NA>              <NA>
## 164                                       Sphingomonas         naasensis
## 165                                             Dongia              <NA>
## 166                                         Reyranella              <NA>
## 167                                       Pseudolabrys              <NA>
## 168                                               <NA>              <NA>
## 169                                        Sphingobium              <NA>
## 170                                        Caulobacter              <NA>
## 171                                    Solirubrobacter              <NA>
## 172                                               <NA>              <NA>
## 173                                         Galbitalea              <NA>
## 174                                   Mucilaginibacter              <NA>
## 175                                           Bacillus              <NA>
## 176                                               <NA>              <NA>
## 177                                               <NA>              <NA>
## 178                                               <NA>              <NA>
## 179                                               <NA>              <NA>
## 180                                            Gemmata              <NA>
## 181                                               <NA>              <NA>
## 182                                         Terrimonas              <NA>
## 183                                               <NA>              <NA>
## 184                                      Edaphobaculum              <NA>
## 185                                           Coxiella              <NA>
## 186                                               <NA>              <NA>
## 187                                       Alkanibacter              <NA>
## 188                                               <NA>              <NA>
## 189                                               <NA>              <NA>
## 190                                               <NA>              <NA>
## 191         Burkholderia-Caballeronia-Paraburkholderia              <NA>
## 192                                               <NA>              <NA>
## 193                                         Variovorax              <NA>
## 194                                        Ferrovibrio              soli
## 195                                               <NA>              <NA>
## 196                     Methylobacterium-Methylorubrum              <NA>
## 197                                              Bosea       thiooxidans
## 198                                              Bosea              <NA>
## 199                                         Tardiphaga          robiniae
## 200                                           Starkeya              <NA>
## 201                                     Hyphomicrobium              <NA>
## 202                                       Sphingopyxis              <NA>
## 203                                 Altererythrobacter              <NA>
## 204                                      Mesorhizobium              <NA>
## 205                                       Conexibacter              <NA>
## 206                                   Pajaroellobacter              <NA>
## 207                                   Pajaroellobacter              <NA>
## 208                                          Sorangium              <NA>
## 209                                               <NA>              <NA>
## 210                                  Promicromonospora              <NA>
## 211                                          Leifsonia              <NA>
## 212                                               <NA>         aoyamense
## 213                                          Agromyces              <NA>
## 214                                      Mycobacterium              <NA>
## 215                                       Herbidospora      mongoliensis
## 216                                         Nonomuraea              <NA>
## 217                                     Actinocorallia              <NA>
## 218                                       Streptomyces              <NA>
## 219                                         Pedobacter              <NA>
## 220                                               <NA>              <NA>
## 221                                               <NA>              <NA>
## 222                                      Paenibacillus            lautus
## 223                                      Paenibacillus              <NA>
## 224                                      Paenibacillus              <NA>
## 225                                      Paenibacillus              <NA>
## 226                                      Paenibacillus              <NA>
## 227                                      Paenibacillus              <NA>
## 228                                       Domibacillus              <NA>
## 229                                           Bacillus              <NA>
## 230                                     Lysinibacillus              <NA>
## 231                                     Lysinibacillus              <NA>
## 232                                     Terrimicrobium              <NA>
## 233                                     Terrimicrobium              <NA>
## 234                                     Terrimicrobium              <NA>
## 235                                     Chthoniobacter              <NA>
## 236                                     Chthoniobacter              <NA>
## 237                                   Verrucomicrobium          spinosum
## 238                                            Gemmata              <NA>
## 239                                     Singulisphaera              <NA>
## 240                                       Edaphobacter              <NA>
## 241                                       Ohtaekwangia              <NA>
## 242                                       Ohtaekwangia              <NA>
## 243                                   Pseudoflavitalea              <NA>
## 244                                   Pseudoflavitalea              <NA>
## 245                                   Pseudoflavitalea              <NA>
## 246                                          Niastella              <NA>
## 247                                          Niastella           hibisci
## 248                                          Niastella              <NA>
## 249                                          Niastella              <NA>
## 250                                         Flavitalea              <NA>
## 251                                       Chitinophaga      ginsengihumi
## 252                                       Chitinophaga       arvensicola
## 253                                       Chitinophaga              soli
## 254                                       Chitinophaga              <NA>
## 255                                       Chitinophaga              <NA>
## 256                                         Taibaiella              <NA>
## 257                                               <NA>              <NA>
## 258                                     Steroidobacter              <NA>
## 259                                        Acidibacter              <NA>
## 260                                        Acidibacter              <NA>
## 261                                        Acidibacter              <NA>
## 262                                         Tahibacter              <NA>
## 263                                        Xanthomonas              <NA>
## 264                                               <NA>              <NA>
## 265                                               <NA>              <NA>
## 266                                           Massilia         armeniaca
## 267                                               <NA>              <NA>
## 268                                    Pseudoduganella              <NA>
## 269                                    Pseudoduganella           eburnea
## 270                                           Massilia              <NA>
## 271                                           Massilia              <NA>
## 272                                        Cupriavidus              <NA>
## 273                                        Cupriavidus              <NA>
## 274                                      Achromobacter              <NA>
## 275                                               <NA>         paradoxus
## 276                                         Xylophilus              <NA>
## 277                                        Rhizobacter              <NA>
## 278                                       Sphingomonas       mucosissima
## 279                                         Reyranella              <NA>
## 280                                         Microvirga              <NA>
## 281 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium              <NA>
## 282                                            Devosia         neptuniae
## 283                                           Shinella              <NA>
## 284                                               <NA>              <NA>
## 285                                               <NA>              <NA>
## 286                                            Ensifer              <NA>
## 287 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium              <NA>
## 288                                       Neorhizobium              <NA>
## 289 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium       azooxidifex
## 290                                               <NA>              <NA>
## 291                                   Phenylobacterium            mobile
## 292                                         Haliangium              <NA>
## 293                                   Pajaroellobacter              <NA>
## 294                                 Cellulosimicrobium              <NA>
## 295                                     Microbacterium              <NA>
## 296                                      Mycobacterium              <NA>
## 297                                         Glycomyces              <NA>
## 298                                       Streptomyces              <NA>
## 299                                       Streptomyces              <NA>
## 300                                       Streptomyces              <NA>
## 301                                               <NA>              <NA>
## 302                                         Pedobacter      panaciterrae
## 303                                     Roseimicrobium              <NA>
## 304                                       Ohtaekwangia              <NA>
## 305                                       Ohtaekwangia              <NA>
## 306                                       Ohtaekwangia              <NA>
## 307                                       Ohtaekwangia              <NA>
## 308                                     Flavobacterium              <NA>
## 309                                   Chryseobacterium ginsenosidimutans
## 310                                   Chryseobacterium              <NA>
## 311                                         Flavitalea              <NA>
## 312                                          Niastella              <NA>
## 313                                          Niastella              <NA>
## 314                                   Pseudoflavitalea              <NA>
## 315                                       Chitinophaga              <NA>
## 316                                       Chitinophaga              <NA>
## 317                                       Chitinophaga          humicola
## 318                                       Chitinophaga              <NA>
## 319                                       Chitinophaga          pinensis
## 320                                       Chitinophaga              <NA>
## 321                                       Chitinophaga              <NA>
## 322                                       Chitinophaga              <NA>
## 323                                       Chitinophaga              <NA>
## 324                                        Dyadobacter              <NA>
## 325                                     Steroidobacter    agariperforans
## 326                                  Pseudoxanthomonas              <NA>
## 327                                   Stenotrophomonas              <NA>
## 328                                   Stenotrophomonas              <NA>
## 329                                         Lysobacter              <NA>
## 330                                         Lysobacter              <NA>
## 331                                               <NA>              <NA>
## 332                                         Legionella              <NA>
## 333                                        Pseudomonas              <NA>
## 334                                        Pseudomonas              <NA>
## 335                                        Pseudomonas              <NA>
## 336                                        Pseudomonas              <NA>
## 337                                        Pseudomonas              <NA>
## 338                                         Klebsiella              <NA>
## 339                                               <NA>              <NA>
## 340                                               <NA>              <NA>
## 341                                               <NA>              <NA>
## 342                                        Cupriavidus     metallidurans
## 343         Burkholderia-Caballeronia-Paraburkholderia              <NA>
## 344                                               <NA>              <NA>
## 345                                      Achromobacter              <NA>
## 346                             GKS98 freshwater group              <NA>
## 347                                         Caenimonas              <NA>
## 348                                       Sphingomonas              <NA>
## 349                                       Sphingomonas              <NA>
## 350                                         Hephaestia              <NA>
## 351                                        Ferrovibrio              <NA>
## 352                                         Reyranella              <NA>
## 353                                         Reyranella              <NA>
## 354                                               <NA>              <NA>
## 355                                            Kaistia           adipata
## 356                                               <NA>              <NA>
## 357                                         Microvirga              <NA>
## 358                     Methylobacterium-Methylorubrum          jeotgali
## 359                                               <NA>              <NA>
## 360                                     Bradyrhizobium              <NA>
## 361                                               <NA>              <NA>
## 362                                     Hyphomicrobium              <NA>
## 363                                 Altererythrobacter              <NA>
## 364                                            Devosia              <NA>
## 365                                    Phyllobacterium              <NA>
## 366                                               <NA>              <NA>
## 367                                        Caulobacter     haematophilum
## 368                                   Phenylobacterium        conjunctum
## 369                                               <NA>              <NA>
## 370                                               <NA>              <NA>
## 371                                       Conexibacter              <NA>
## 372                                               <NA>              <NA>
## 373                                             KD3-10              <NA>
## 374                                         Myxococcus              <NA>
## 375                                         Archangium              <NA>
## 376                                      Phaselicystis              <NA>
## 377                                       Bdellovibrio     bacteriovorus
## 378                                      Cutibacterium              <NA>
## 379                                      Aeromicrobium              <NA>
## 380                                          Kribbella              <NA>
## 381                                              Iamia              <NA>
## 382                                       Cellulomonas              <NA>
## 383                                          Oerskovia              <NA>
## 384                                          Leifsonia              <NA>
## 385                                     Microbacterium              <NA>
## 386                                           Hamadaea              <NA>
## 387                                       Actinoplanes    atraurantiacus
## 388                                               <NA>              <NA>
## 389                                      Amycolatopsis              <NA>
## 390                                       Herbidospora              <NA>
## 391                                       Streptomyces              <NA>
## 392                                       Streptomyces              <NA>
## 393                                               <NA>              <NA>
## 394                                   Sphingobacterium              <NA>
## 395                                   Sphingobacterium              <NA>
## 396                                   Mucilaginibacter              <NA>
## 397                                   Mucilaginibacter              <NA>
## 398                                               <NA>              <NA>
## 399                                               <NA>              <NA>
## 400                                  Levilactobacillus              <NA>
## 401                                Fructilactobacillus              <NA>
## 402                                Fructilactobacillus              <NA>
## 403                                Lactiplantibacillus              <NA>
## 404                                      Paenibacillus              <NA>
## 405                                               <NA>              <NA>
## 406                                               <NA>              <NA>
## 407                                     Terrimicrobium              <NA>
## 408                                     Terrimicrobium              <NA>
## 409                                     Terrimicrobium              <NA>
## 410                                     Terrimicrobium              <NA>
## 411                                     Terrimicrobium              <NA>
## 412                                      Luteolibacter    gellanilyticus
## 413                                               <NA>              <NA>
## 414                                               <NA>              <NA>
## 415                                               <NA>              <NA>
## 416                                          Hassallia              <NA>
## 417                                               <NA>              <NA>
## 418                                       Ohtaekwangia              <NA>
## 419                                       Ohtaekwangia              <NA>
## 420                                   Pseudoflavitalea              <NA>
## 421                                          Niastella              <NA>
## 422                                          Niastella              <NA>
## 423                                       Chitinophaga              <NA>
## 424                                       Chitinophaga              <NA>
## 425                                       Chitinophaga              <NA>
## 426                                               <NA>              <NA>
## 427                                        Dyadobacter      ginsengisoli
## 428                                               <NA>              <NA>
## 429                                               <NA>              <NA>
## 430                                        Acidibacter              <NA>
## 431                                               <NA>              <NA>
## 432                                  Pseudoxanthomonas         helianthi
## 433                                        Xanthomonas              <NA>
## 434                                         Lysobacter              <NA>
## 435                                               <NA>              <NA>
## 436                                         Dokdonella              <NA>
## 437                                           Coxiella              <NA>
## 438                                               <NA>              <NA>
## 439                                        Pseudomonas              <NA>
## 440                                        Pseudomonas              <NA>
## 441                                        Pseudomonas              <NA>
## 442                                        Pseudomonas              <NA>
## 443                                        Pseudomonas              <NA>
## 444                               Escherichia-Shigella              <NA>
## 445                                            Pantoea              <NA>
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levels(ps.m$Phylum)
##  [1] "Abditibacteriota"  "Acidobacteriota"   "Actinobacteriota" 
##  [4] "Armatimonadota"    "Bacteroidota"      "Bdellovibrionota" 
##  [7] "Campylobacterota"  "Chloroflexi"       "Crenarchaeota"    
## [10] "Cyanobacteria"     "Dependentiae"      "Desulfobacterota" 
## [13] "Elusimicrobiota"   "Entotheonellaeota" "Fibrobacterota"   
## [16] "Firmicutes"        "Gemmatimonadota"   "MBNT15"           
## [19] "Myxococcota"       "Nitrospirota"      "Patescibacteria"  
## [22] "Planctomycetota"   "Proteobacteria"    "RCP2-54"          
## [25] "Spirochaetota"     "Sumerlaeota"       "Verrucomicrobiota"

Несколько картинок по динамике предсталенности отдельных фил Bdellovibrionota - хищники, индикатор развитого сообщества

ps.m %>% 
  filter(Phylum == "Bdellovibrionota") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Myxococcota - вроде бы тоже, но как нам известно могут быть целлулотитиками

ps.m %>% 
  filter(Phylum == "Myxococcota") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Археи появляются тоже на поздних стадиях - вообще я бы хотел бы опять развить тему важности азотного метаболизма на поздних стадиях разложения.
Оч хочется метагеном, но не этот.
Кроме того хочется отметить, что эти минорные группы возникают на D12

ps.m %>% 
  filter(Phylum == "Crenarchaeota") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Gammaproteobacteria - они треть кластера blue

ps.m %>% 
  filter(Class == "Gammaproteobacteria") %>% 
  group_by(Description, Day) %>% 
  summarise(Bs = sum(Abundance)) %>% 
  ggplot() +
  geom_boxplot(aes(x = Day, y = Bs)) +
  theme_bw()
## `summarise()` has grouped output by 'Description'. You can override using the
## `.groups` argument.

Все филы - представлененось логорифмирована по основанию 2 - что-то не очень.

ps.m %>% 
  group_by(Description, Day, Phylum) %>% 
  summarise(Bs = log2(sum(Abundance))) %>% 
  ggplot(aes(x = Day, y = Bs)) +
  geom_boxplot() +
  theme_bw() +
  facet_wrap(~ Phylum)
## `summarise()` has grouped output by 'Description', 'Day'. You can override
## using the `.groups` argument.
## Warning: Removed 488 rows containing non-finite values (stat_boxplot).